I already asked if there are more rationals than integers here...
Are there more rational numbers than integers?
However, there is one particular argument that I didn't give before which I still find compelling...
Every integer is also a rational. There exist (many) rationals that are not integers. Therefore there are more rationals than integers.
Obviously, in a sense, I am simply choosing one particular bijection, so by the definition of set cardinality this argument is irrelevant. But it's still a compelling argument for "size" because it's based on a trivial/identity bijection.
EDIT please note that the above paragraph indicates that I know about set cardinality and how it is defined, and accept it as a valid "size" definition, but am asking here about something else.
To put it another way, the set of integers is a proper subset of the set of rationals. It seems strange to claim that the two sets are equal in size when one is a proper subset of the other.
Is there, for example, some alternative named "size" definition consistent with the partial ordering given by the is-a-proper-subset-of operator?
EDIT clearly it is reasonable to define such a partial order and evaluate it. And while I've use geometric analogies, clearly this is pure set theory - it depends only on the relevant sets sharing members, not on what the sets represent.
Helpful answers might include a name (if one exists), perhaps for some abstraction that is consistent with this partial order but defined in cases where the partial order is not. Even an answer like "yes, that's valid, but it isn't named and doesn't lead to any interesting results" may well be correct - but it doesn't make the idea unreasonable.
Sorry if some of my comments aren't appropriate, but this is pretty frustrating. As I said, it feels like I'm violating some kind of taboo.
EDIT - I was browsing through random stuff when I was reminded this was here, and that I actually ran into an example where "size" clearly can't mean "cardinality" fairly recently (actually a very long time ago and many times since, but I didn't notice the connection until recently).
The example relates to closures of sets. Please forgive any wrong terminology, but if I have a seed set of {0} and an operation $f x = x+2$, the closure of that set WRT that operation is the "smallest" set that is closed WRT that operation, meaning that for any member $x$ of the set, $x+2$ must also be a member. So obviously the closure is {0, 2, 4, 6, 8, ...} - the even non-negative integers.
However, the cardinality of the set of even non-negative integers is equal to the cardinality of the set of all integers, or even all rationals. So if "smallest" means "least cardinality", the closure isn't well-defined - the set {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, ...} is no larger than the set {0, 2, 4, 6, 8, ...}.
Therefore, the meaning of "smallest" WRT set closures refers to some measure of size other than cardinality.
I'm not adding this as a late answer because it's already covered by the answers below - it's just a particular example that makes sense to me.
Another addition - while skimming the first chapter of a topology textbook in a library some time ago, IIRC I spotted a definition of the set closure which did not use the word "smallest", and made no direct reference to "size". That led me to think maybe the common "definition" of closures I'm familiar with is just a stopgap for those of us who aren't ready for a formally precise definition.
However, while searching for another source, I instead found this answer to a topology question that uses the word "smallest" in its definition of closure (and "largest" in its "dual definition of interior"). And then I found this answer which describes a concept of size based on partial ordering of topological embeddings. I think that's another example to add to those in answers below.