Where are some interesting places where the axiom of choice crops up in category theory? The two that come to mind are splitting epics in Set and taking the Skel of a category. Surely there are lots of other interesting (and maybe upsetting) places where this comes up.
 A: While not the traditional Axiom of choice, Zorn's Lemma makes an appearance on the road to Mitchel's Theorem;
If X is an abelian category with the sup property(Grothendeick's AB5), then an object E is injective iff it does not have a non-trivial essential extension.
Mitchel's theorem is stated in Rotman's Homological Algebra(page 316) as;
If A is a small abelian category, then there is a covariant full faithful exact functor from A to abelian groups.
I believe(but do not have access to the appropriate materials to give details) that Zorn's lemma appears in homotopy limits also.
A: If $s:\mathcal{X} \to \mathcal{C}$ is a fibered category and $\varphi:C \to D$ is a morphism in $\mathcal{C}$, for each object $y$ in the fiber $\mathcal{X}_D$ the axiom of choice allows us to specify exactly one pullback $f:y_C \to y$ (i.e., a cartesian arrow $f$ with $s(f)=\varphi$).  The choice of such a collection is called a 'cleavage', and a cleavage always exists by the axiom of choice.  
This enables us to define the 'change of base functor' $\varphi^*:\mathcal{X}_D \to \mathcal{X}_C$.  
A: Using the usual definition of "functor," almost any functor
constructed using only universal properties requires the axiom of
choice.  For instance, if a category C has products, then one wants a
"product assigning" functor C×C → C, but in order to define this you
have to choose a product for each pair of objects.  If C is a large
category, then you need an axiom of choice for proper classes.
However, this sort of thing is arguably not a "real" use of the axiom
of choice.  It's more accurate to say that in the absence of the axiom
of choice the usual definition of "functor" is not sufficient, and one
must use anafunctors
instead.  Proving that fully faithful + essentially surjective =
equivalence is the same.  Most often in category theory when we want
to "choose" something, that thing is in fact determined up to unique
isomorphism (though not uniquely on the nose) and in that case using
anafunctors is sufficient to avoid choice.
The axiom of choice does, however, come up in the study of particular
properties of the category Set.  One interesting consequence of the
fact that epics split in Set is that all functors defined on Set
preserve epics.  I think this is an important part of Blass' proof
that the existence of nontrivial (left and right) exact endofunctors
of set is equivalent to the existence of measurable cardinals.
Another interesting consequence is that Set is its own "ex/lex
completion."
A: In proving that whenever there is a full, faithful functor F: C to D which is essentially surjective (i.e. hits every isomorphism class of objects in D), C and D are equivalent categories.
(This is pretty close to your example of taking Skel of a category.)
A: Choosing fiber products to define the sheafification of a presheaf with respect to a grothendieck pretopology (you later prove that this construction is independent of choice, but it's necessary during the construction).  See stacks-git in the remark immediately preceding proposition 8.10.3.
