I liked da one wit da ponies in it.
Yeah I know it sounds like a non-answer, I really can't pick a favorite. If you held a gun to my head I suppose I'd say Luna Eclipsed due to it being the newest, and of course having my favorite characters in it. If anything it'd probably be easier to pick least favorites, and even those are fun. The characters are all endearing (OK, maybe endearing isn't exactly the right word for Gilda), the art and animation are beautiful (I love the trot walk cycle, and the detail put into lip synching, f'rinstance), and overall there's just a sort of sense of joy to it that's not all saccharine phony. It just feels like a labor of love by all involved, and it's sorta infectious.
I mean...yeah, I guess it's okay. For a
girls' show. /spike
EDIT:
And I really like the CMCs, too. I don't get why some people don't like them.
I can make with wild speculation there. I think enough shows/commercials/what-have-yous have too often thrown in kids or baby animals because they're cute by default and are supposed to elicit an automatic "D'AWWWW!" response from audiences, and expect that anticipated cuteness to stand on its own like some sort of magic auto-appeal bullet. So it winds up being that people in actuality get so durned sick of seeing kids and puppies and such tossed in with no effort made that it becomes an automatic turn-off instead. I like the CMCs though. FiM didn't take the lazy way out with the typical lisping, stuttering, "LOOK AT ME AREN'T I JUST SO CUTE?" types, and instead put as much effort into fleshing them out as interesting characters in their own right as they did the rest of the cast.
Call upon the CMC ponies! Scoot-a-loo, Scoot Scoot-a-loo...