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I recall a Sherlock Holmes mystery where the detective and his assistant are in their apartment and Watson is working over some decision that he has to make. Suddenly Holmes pipes in to give his opinion on the matter, which utterly confounds Watson, because Watson had been having the debate with himself internally. Holmes explains that he had watched John throughout the night, and had been able to follow Watson's train of thought as clearly as if Watson had been verbalizing it the whole way.

I just can't remember which case this scene takes place in. Can anyone help me recall it?

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This happens twice in the Sherlock Holmes canon (and once in a very short story, written by Doyle but not usually included in the collected works), openly inspired by Poe's Dupin.

The opening passage of "The Adventure of the Dancing Men", from the collection The Return of Sherlock Holmes (1905), is as follows:

Holmes had been seated for some hours in silence with his long, thin back curved over a chemical vessel in which he was brewing a particularly malodorous product. His head was sunk upon his breast, and he looked from my point of view like a strange, lank bird, with dull grey plumage and a black top-knot.

“So, Watson,” said he, suddenly, “you do not propose to invest in South African securities?”

I gave a start of astonishment. Accustomed as I was to Holmes's curious faculties, this sudden intrusion into my most intimate thoughts was utterly inexplicable.

“How on earth do you know that?” I asked.

He wheeled round upon his stool, with a steaming test-tube in his hand and a gleam of amusement in his deep-set eyes.

“Now, Watson, confess yourself utterly taken aback,” said he.

“I am.”

“I ought to make you sign a paper to that effect.”

“Why?”

“Because in five minutes you will say that it is all so absurdly simple.”

“I am sure that I shall say nothing of the kind.”

“You see, my dear Watson”—he propped his test-tube in the rack and began to lecture with the air of a professor addressing his class—“it is not really difficult to construct a series of inferences, each dependent upon its predecessor and each simple in itself. If, after doing so, one simply knocks out all the central inferences and presents one's audience with the starting-point and the conclusion, one may produce a startling, though possibly a meretricious, effect. Now, it was not really difficult, by an inspection of the groove between your left forefinger and thumb, to feel sure that you did NOT propose to invest your small capital in the goldfields.”

“I see no connection.”

“Very likely not; but I can quickly show you a close connection. Here are the missing links of the very simple chain: 1. You had chalk between your left finger and thumb when you returned from the club last night. 2. You put chalk there when you play billiards to steady the cue. 3. You never play billiards except with Thurston. 4. You told me four weeks ago that Thurston had an option on some South African property which would expire in a month, and which he desired you to share with him. 5. Your cheque-book is locked in my drawer, and you have not asked for the key. 6. You do not propose to invest your money in this manner.”

“How absurdly simple!” I cried.

Early in the controversial story "The Adventure of the Cardboard Box", from the collection Memoirs of Sherlock Holmes (1894), a similar conversation takes place:

Finding that Holmes was too absorbed for conversation I had tossed side the barren paper, and leaning back in my chair I fell into a brown study.Suddenly my companion’s voice broke in upon mythoughts: “You are right, Watson,” said he. “It does seem a most preposterous way of settling a dispute.”

“Most preposterous!” I exclaimed, and then suddenly realizing how he had echoed the inmost thought of my soul, I sat up in my chair and stared at him in blank amazement.

“What is this, Holmes?” I cried. “This is beyond anything which I could have imagined.”

He laughed heartily at my perplexity. “You remember,” said he, “that some little time ago when I read you the passage in one of Poe’s sketches in which a close reasoner follows the unspoken thoughts of his companion, you were inclined to treat the matter as a mere tour-de-force of the author. On my remarking that I was constantly in the habit of doing the same thing you expressed incredulity.”

[...]

“Then I will tell you. After throwing down your paper, which was the action which drew my attention to you, you sat for half a minute with a vacant expression. Then your eyes fixed themselves upon your newly framed picture of General Gordon, and I saw by the alteration in your face that a train of thought had been started. But it did not lead very far. Your eyes flashed across to the unframed portrait of Henry Ward Beecher which stands upon the top of your books. Then you glanced up at the wall, and of course your meaning was obvious. You were thinking that if the portrait were framed it would just cover that bare space and correspond with Gordon’s picture there.”

“You have followed me wonderfully!” I exclaimed.

“So far I could hardly have gone astray. But now your thoughts went back to Beecher, and you looked hard across as if you were studying the character in his features. Then your eyes ceased to pucker, but you continued to look across, and your face was thoughtful. You were recalling the incidents of Beecher’s career. I was well aware that you could not do this without thinking of the mission which he undertook on behalf of the North at the time of the Civil War, for I remember your expressing your passionate indignation at the way in which he was received by the more turbulent of our people. You felt so strongly about it that I knew you could not think of Beecher without thinking of that also. When a moment later I saw your eyes wander away from the picture, I suspected that your mind had now turned to the Civil War, and when I observed that your lips set, your eyes sparkled, and your hands clenched I was positive that you were indeed thinking of the gallantry which was shown by both sides in that desperate struggle. But then, again, your face grew sadder, you shook your head. You were dwelling upon the sadness and horror and useless waste of life. Your hand stole towards your own old wound and a smile quivered on your lips, which showed me that the ridiculous side of this method of settling international questions had forced itself upon your mind. At this point I agreed with you that it was preposterous and was glad to find that all my deductions had been correct.”

A commenter informed me of another Sherlock Holmes story, written by Doyle but so short (a single scene) that it is usually not counted as part of "the canon", in which the same trick is used. The entire text of this story, "The Field Bazaar", is not much more than the following:

"I should certainly do it," said Sherlock Holmes.

I started at the interruption, for my companion had been eating his breakfast with his attention entirely centered upon the paper which was propped up by the coffee pot. Now I looked across at him to find his eyes fastened upon me with the half-amused, half-questioning expression which he usually assumed when he felt he had made an intellectual point.

[...]

"I may be very obtuse," said I, "but I confess that I am unable to see how you have managed to know that I was... I was..."

"Asked to help in the Edinburgh University Bazaar..."

"Precisely. The letter has only just come to hand, and I have not spoken to you since."

"In spite of that," said Holmes, leaning back in his chair and putting his finger tips together, "I would even venture to suggest that the object of the bazaar is to enlarge the University cricket field."

I looked at him in such bewilderment that he vibrated with silent laughter.

[...]

"I fear that my good nature in giving explanations has seriously compromised my reputation," said Holmes. "But in this case the train of reasoning is based upon such obvious facts that no credit can be claimed for it. You entered the room with a thoughtful expression, the expression of a man who is debating some point in his mind. In your hand you held a solitary letter. Now last night you retired in the best of spirits, so it was clear that it was this letter in your hand which had caused the change in you."

"This is obvious."

"It is all obvious when it is explained to you. I naturally asked myself what the letter could contain which might have this effect upon you. As you walked you held the flap side of the envelope towards me, and I saw upon it the same shield-shaped device which I have observed upon your old college cricket cap. It was clear, then, that the request came from Edinburgh University — or from some club connected with the University. When you reached the table you laid down the letter beside your plate with the address uppermost, and you walked over to look at the framed photograph upon the left of the mantelpiece."

It amazed me to see the accuracy with which he had observed my movements. "What next?" I asked.

"I began by glancing at the address, and I could tell, even at the distance of six feet, that it was an unofficial communication. This I gathered from the use of the word 'Doctor' upon the address, to which, as a Bachelor of Medicine, you have no legal claim. I knew that University officials are pedantic in their correct use of titles, and I was thus enabled to say with certainty that your letter was unofficial. When on your return to the table you turned over your letter and allowed me to perceive that the enclosure was a printed one, the idea of a bazaar first occurred to me. I had already weighed the possibility of its being a political communication, but this seemed improbable in the present stagnant conditions of politics.

"When you returned to the table your face still retained its expression and it was evident that your examination of the photograph had not changed the current of your thoughts. In that case it must itself bear upon the subject in question. I turned my attention to the photograph, therefore, and saw at once that it consisted of yourself as a member of the Edinburgh University Eleven, with the pavillion and cricket field in the background. My small experience of cricket clubs has taught me that next to churches and cavalry ensigns they are the most debt-laden things upon earth. When upon your return to the table I saw you take out your pencil and draw lines upon the envelope, I was convinced that your were endeavoring to realise some projected improvement which was to be brought about by a bazaar. Your face still showed some indecision, so that I was able to break in upon you with my advice that you should assist in so good an object."

I could not help smiling at the extreme simplicity of his explanation.

"Of course, it was as easy as possible," said I.

My remark appeared to nettle him.

"I may add," said he, "that the particular help which you have been asked to give was that you should write in their album, and that you have already made up your mind that the present incident will be the subject of your article."

"But how—!" I cried.

"It is as easy as possible," said he, "and I leave its solution to your own ingenuity. In the meantime," he added, rasing his paper, "you will excuse me if I return to this very interesting article upon the trees of Cremona, and the exact reasons for the pre-eminence in the manufacture of violins. It is one of those small outlying problems to which I am sometimes tempted to direct my attention."

It's worth noting that, way back in the very first Sherlock Holmes story A Study in Scarlet, Holmes makes reference to this trick as used by Poe, but with a very different tone:

Sherlock Holmes rose and lit his pipe. "No doubt you think that you are complimenting me in comparing me to Dupin," he observed. "Now, in my opinion, Dupin was a very inferior fellow. That trick of his of breaking in on his friends' thoughts with an apropos remark after a quarter of an hour's silence is really very showy and superficial. He had some analytical genius, no doubt; but he was by no means such a phenomenon as Poe appeared to imagine."

For completeness, I include here the passage from Edgar Allan Poe's first Dupin story The Murders in the Rue Morgue which inspired Arthur Conan Doyle to write similar scenes for his own detective character:

We were strolling one night down a long dirty street in the vicinity of the Palais Royal. Being both, apparently, occupied with thought, neither of us had spoken a syllable for fifteen minutes at least. All at once Dupin broke forth with these words:

“He is a very little fellow, that’s true, and would do better for the Théâtre des Variétés.”

“There can be no doubt of that,” I replied unwittingly, and not at first observing (so much had I been absorbed in reflection) the extraordinary manner in which the speaker had chimed in with my meditations. In an instant afterward I recollected myself, and my astonishment was profound.

“Dupin,” said I, gravely, “this is beyond my comprehension. I do not hesitate to say that I am amazed, and can scarcely credit my senses. How was it possible you should know I was thinking of ——-?” Here I paused, to ascertain beyond a doubt whether he really knew of whom I thought.

—“of Chantilly,” said he, “why do you pause? You were remarking to yourself that his diminutive figure unfitted him for tragedy.”

This was precisely what had formed the subject of my reflections. Chantilly was a quondam cobbler of the Rue St. Denis, who, becoming stage-mad, had attempted the rôle of Xerxes, in Crébillon’s tragedy so called, and been notoriously Pasquinaded for his pains.

“Tell me, for Heaven’s sake,” I exclaimed, “the method—if method there is—by which you have been enabled to fathom my soul in this matter.” In fact I was even more startled than I would have been willing to express.

“It was the fruiterer,” replied my friend, “who brought you to the conclusion that the mender of soles was not of sufficient height for Xerxes et id genus omne.”

“The fruiterer!—you astonish me—I know no fruiterer whomsoever.”

“The man who ran up against you as we entered the street—it may have been fifteen minutes ago.”

I now remembered that, in fact, a fruiterer, carrying upon his head a large basket of apples, had nearly thrown me down, by accident, as we passed from the Rue C —— into the thoroughfare where we stood; but what this had to do with Chantilly I could not possibly understand.

There was not a particle of charlatanerie about Dupin. “I will explain,” he said, “and that you may comprehend all clearly, we will first retrace the course of your meditations, from the moment in which I spoke to you until that of the rencontre with the fruiterer in question. The larger links of the chain run thus—Chantilly, Orion, Dr. Nichols, Epicurus, Stereotomy, the street stones, the fruiterer.”

There are few persons who have not, at some period of their lives, amused themselves in retracing the steps by which particular conclusions of their own minds have been attained. The occupation is often full of interest and he who attempts it for the first time is astonished by the apparently illimitable distance and incoherence between the starting-point and the goal. What, then, must have been my amazement when I heard the Frenchman speak what he had just spoken, and when I could not help acknowledging that he had spoken the truth. He continued:

“We had been talking of horses, if I remember aright, just before leaving the Rue C ——. This was the last subject we discussed. As we crossed into this street, a fruiterer, with a large basket upon his head, brushing quickly past us, thrust you upon a pile of paving stones collected at a spot where the causeway is undergoing repair. You stepped upon one of the loose fragments, slipped, slightly strained your ankle, appeared vexed or sulky, muttered a few words, turned to look at the pile, and then proceeded in silence. I was not particularly attentive to what you did; but observation has become with me, of late, a species of necessity.

“You kept your eyes upon the ground—glancing, with a petulant expression, at the holes and ruts in the pavement, (so that I saw you were still thinking of the stones,) until we reached the little alley called Lamartine, which has been paved, by way of experiment, with the overlapping and riveted blocks. Here your countenance brightened up, and, perceiving your lips move, I could not doubt that you murmured the word ‘stereotomy,’ a term very affectedly applied to this species of pavement. I knew that you could not say to yourself ‘stereotomy’ without being brought to think of atomies, and thus of the theories of Epicurus; and since, when we discussed this subject not very long ago, I mentioned to you how singularly, yet with how little notice, the vague guesses of that noble Greek had met with confirmation in the late nebular cosmogony, I felt that you could not avoid casting your eyes upward to the great nebula in Orion, and I certainly expected that you would do so. You did look up; and I was now assured that I had correctly followed your steps. But in that bitter tirade upon Chantilly, which appeared in yesterday’s ‘Musée,’ the satirist, making some disgraceful allusions to the cobbler’s change of name upon assuming the buskin, quoted a Latin line about which we have often conversed. I mean the line

Perdidit antiquum litera sonum.

“I had told you that this was in reference to Orion, formerly written Urion; and, from certain pungencies connected with this explanation, I was aware that you could not have forgotten it. It was clear, therefore, that you would not fail to combine the two ideas of Orion and Chantilly. That you did combine them I saw by the character of the smile which passed over your lips. You thought of the poor cobbler’s immolation. So far, you had been stooping in your gait; but now I saw you draw yourself up to your full height. I was then sure that you reflected upon the diminutive figure of Chantilly. At this point I interrupted your meditations to remark that as, in fact, he was a very little fellow—that Chantilly—he would do better at the Théâtre des Variétés.”

There is no doubt that this is the passage which inspired Doyle and Holmes, because in "The Adventure of the Cardboard Box" Watson mentioned that in the passage which Holmes read to him, "If I remember right, [Poe's character] stumbled over a heap of stones, looked up at the stars, and so on."

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    Now THAT is an answer. Thank you. These were exactly the moments from the Sherlock Holmes cases I was remembering, and this is wonderful having the original example in Poe's work as well. Thank you very much! Commented Sep 1, 2020 at 22:51
  • You're welcome! It was fun to dig into this and gather together all the different instances of this "following internal thought process" trick that I've seen from both Holmes and Dupin, plus confirming the connection between the two.
    – Rand al'Thor
    Commented Sep 1, 2020 at 23:01
  • Why is Watson's chequebook locked in Sherlock's drawer? I know he works for Sherlock but this seems pretty controlling.
    – cxrodgers
    Commented Jun 29, 2021 at 20:28
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    @cxrodgers He doesn't work for him - they're flatmates. At a guess, maybe there's only one safe locked drawer and Holmes happens to be the one with the key, or maybe it's a temporary thing. Reading nefariousness into the relationship between Holmes and Watson seems to be a very modern phenomenon.
    – Rand al'Thor
    Commented Jun 30, 2021 at 4:43
  • @Randal'Thor Wonderful answer; collecting all instances of Holmes' (and even Dupin's) mind-reading . May I suggest to add one more? A.C.D. wrote a short Holmes and Watson scene as a charity work, it features mind-reading and would make a good addition here.
    – Martin
    Commented Oct 13, 2023 at 15:33

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