Solved
Map:
Individual Puzzles:
As per @Henkie's post, the second door from EXAMPLE ROOM solved
On the first page, the right side is encoded as morse.
It reads SEVENBIGJSMALLASMALLBBIGA
Which leads to 7JabA (COLLISIONS)
COLLISIONS solved
Each paragraph describes one of the individuals who are particles...
1st J/psi meson J
2nd proton p
3rd B meson B
4th Kaon K
5th Lambda baryon Λ, wearing a belt: A
yielding JpBKA (REASSEMBLY)
REASSEMBLY solved
The correct solution (from Henkie) was HAF/DCI/EBG.
GET TWO FREE solved
There are three sudoku: a cyan one, a magenta one, and a yellow one
(blue=magenta+cyan; green=cyan+yellow; red=magenta+yellow; black=magenta+cyan+yellow).
The exit wall is repeated cyan, magenta and yellow pixels (could there be three rooms or is that just a hint for the colours employed?)
There is a grey 2 at the top-right of the bottom-right block - do we need to also "get this free"?
If I got it all right, then all three are uniquely solvable with the grey 2, without it: Cyan has 38 solutions (only one has a 2 there, 20 have a 4, 11 have a 5, 6 have a 9); Magenta still has just the one solution; Yellow has 4 solutions, the other three having a 1 in the grey 2's place.
The sudokus, with solutions using the grey 2 on the right.
Cyan: .7..1.2.....7....86..592....52.348....1...3....468.12....361...1....7.....6.2..3.
· 7 · | · 1 · | 2 · · 4 7 9 | 8 1 3 | 2 6 5
· · · | 7 · · | · · 8 2 3 5 | 7 4 6 | 9 1 8
6 · · | 5 9 2 | · · · 6 1 8 | 5 9 2 | 4 7 3
------+-------+------ ------+-------+------
· 5 2 | · 3 4 | 8 · · 7 5 2 | 1 3 4 | 8 9 6
· · 1 | · · · | 3 · · 8 6 1 | 2 7 9 | 3 5 4
· · 4 | 6 8 · | 1 2 · 3 9 4 | 6 8 5 | 1 2 7
------+-------+------ ------+-------+------
· · · | 3 6 1 | · · · 9 8 7 | 3 6 1 | 5 4 2
1 · · | · · 7 | · · · 1 2 3 | 4 5 7 | 6 8 9
· · 6 | · 2 · | · 3 · 5 4 6 | 9 2 8 | 7 3 1
Magenta: .....2.1.136......7.451.6.....2..571...495...582..1.....5.497........846.4.8.....
· · · | · · 2 | · 1 · 9 5 8 | 6 7 2 | 4 1 3
1 3 6 | · · · | · · · 1 3 6 | 9 8 4 | 2 5 7
7 · 4 | 5 1 · | 6 · · 7 2 4 | 5 1 3 | 6 8 9
------+-------+------ ------+-------+------
· · · | 2 · · | 5 7 1 4 9 3 | 2 6 8 | 5 7 1
· · · | 4 9 5 | · · · 6 7 1 | 4 9 5 | 3 2 8
5 8 2 | · · 1 | · · · 5 8 2 | 7 3 1 | 9 6 4
------+-------+------ ------+-------+------
· · 5 | · 4 9 | 7 · · 8 6 5 | 1 4 9 | 7 3 2
· · · | · · · | 8 4 6 2 1 9 | 3 5 7 | 8 4 6
· 4 · | 8 · · | · · · 3 4 7 | 8 2 6 | 1 9 5
Yellow: ......6144....8.35213.6.....94..1...8.......6...8..49.....7.84.12.4....7745......
· · · | · · · | 6 1 4 5 8 7 | 3 9 2 | 6 1 4
4 · · | · · 8 | · 3 5 4 6 9 | 7 1 8 | 2 3 5
2 1 3 | · 6 · | · · · 2 1 3 | 5 6 4 | 7 8 9
------+-------+------ ------+-------+------
· 9 4 | · · 1 | · · · 3 9 4 | 6 2 1 | 5 7 8
8 · · | · · · | · · 6 8 5 1 | 9 4 7 | 3 2 6
· · · | 8 · · | 4 9 · 6 7 2 | 8 5 3 | 4 9 1
------+-------+------ ------+-------+------
· · · | · 7 · | 8 4 · 9 3 6 | 1 7 5 | 8 4 2
1 2 · | 4 · · | · · 7 1 2 8 | 4 3 6 | 9 5 7
7 4 5 | · · · | · · · 7 4 5 | 2 8 9 | 1 6 3
If we were to overlay those on the right there would be FIVE black numbers:
. · · · | · · · | · · · 6
7 · · · | · · · | · · · ?
@ · · · | 5 · · | · · · H
------+-------+------
I · · · | · · · | · · · Q
R · · 1 | · · · | 3 · · Z
[ · · · | · · · | · · · c
------+-------+------
d · · · | · · · | · · 2 l
m · · · | · · · | · · · u
v · 4 · | · · · | · · · ~
All the letters on the right are 8 more (in ASCII) than those on the left, so the numbers 1,2,3,4,5 yield TlXwC (MAZES IN MAZES)
MAZES IN MAZES solved
Note that you start by entering Red and inside Red you enter a Yellow then inside that Yellow you enter another copy of Yellow then pop back out of that Yellow into the previous Yellow then out of that Yellow back to the original Red then ... then you exit the maze from the original Red:
yielding Ue3b6
HALF THE PICTURE solved
XORing the Reassembly image with the Half image, we get 
. Reading off the red, green, and blue channels, we get:
C1en2 (MIND GAMES)
2bzyR (BACKTRACKING)
k5E2V (BLOCK CIPHER)
MIND GAMES solved
This is a game of Mastermind: the blues represent misses, the reds are hits but in the wrong place, and the greens are hits but in the right place. The solution is DtvqW.
WHERE ARE YOU? solved
That $\oplus$ symbol is "xor" (the operation where you take the bits in either A or B but not both; if you're xoring several things together it doesn't matter what order you do them in.). The equation says that xoring all three of the rooms together gives us 4sP~u; since you can undo an XOR with another XOR, I just XORed all three 5-char strings together to get LahLf.
ILL OMENS solved
These characters are a Unicode text file reinterpreted as extended ASCII. Reading off the Unicode characters, most are from the Sutton Sign Language block; these, plus modifiers to label capital and lowercase, spell r2HDr.
ACCOLADES solved
These are all descriptions of Stack Exchange badges! The badges, in order, are Revival, Research Assistant, and Populist. Extracting the letters, makes "ARAPANOVECV - 6". Applying a Caesar shift of -6 results in "ULUJUHIPYWP", which is the red key.
BACKTRACKING solved
There is a gray character hidden (or sometimes not hidden) in each of the puzzles on this path. Those characters, in reverse order, are Qv2RX (GOAL IN SIGHT).
GOAL IN SIGHT solved
The images refer to other "visual" puzzles, the numbers refer to puzzle solutions (from left to right):
H : A well balanced puzzle: Logic puzzle(s) in visual disguise
P : Perplexing Fireworks
B : Hidden Message: Of Shapes and Numbers
W : Lepidopterology needed!
S : The Writing's on the Wall
B : A hunt for long forgotten treasure ...but beware the pirate's curse!
D : Find the secret phrase in this encrypted image (Part 4)
R : The Musing Of the Eggs
B : The markings of Mictal
U : This is important. I need you to listen…
O : Little bits of food
So the green key is HPBWSBDRBUO.
BLOCK CIPHER solved
This is a screenshot from Minecraft. Each block in Minecraft has a "data value", a number used internally to store what type of block is in which location. Reading the data values of the blocks in a row out as ASCII gives 14k9p (MULTIPLE PARTS).
BLOCK CIPHER (solution 2)
If you read the IDs of the lower blocks you get "Red5T0nE". Using a DES cipher on the base64 sign text with this as the key gives you nCXwy (FIFTEEN PUZZLES).
MULTIPLE PARTS solved
Both clues refer to Stack Exchange puzzles that have been duplicated in format by many people. The first refers to The hangman game backward and the second refers to The Security to the Party. Extracting the letters we're told to from each of the question titles, we get EWNCGGMESRO+5. Applying a Caesar shift of +5 makes JBSHLLRJXWT, which is the blue key.
FIFTEEN PUZZLES solved
Each of the puzzles has a 4x4 grid with a square missing in the bottom right corner. These can be treated as scrambled 15-puzzles, and the arrows here tell us how they were scrambled. Undoing the scrambles, we get... nothing really. But, if you then undo the scramble of ALL the solved puzzles using the last arrow as a reference, you get: 
This looks like 4w9g8, and in fact it is. (TAKING IT APART)
TAKING IT APART solved
Deciphering "APLASTICBAG" with the keys yields:
red: GERRYMANDER
green: TAKEASFLAGS
blue: ROTTHIRTEEN
So we gerrymander to put 3 of four regions in Greens favour (currently way behind Red in the polls)
Then treat the lines as flags as per semaphore in the direction their region's number is facing
Then rot 13 the letters
Yielding:
Reading those in the direction of the region numbers gives us:
GOOD JOB YOU HAVE FINISHED THE MAZE (!)
