I think it’s pretty clear from even a casual perusal of this blog that Fluttershy is my favorite; I’ve outright stated it several times. And practically any fan has a quick and ready answer for the “Best pony?” question.
But (and maybe I’m alone in this, or maybe it’s a common problem) picking my second-favorite is a lot harder. Pinkie makes me laugh. Twilight reminds me of myself (though in a different way from, and not as strongly as, Fluttershy). Rarity is interestingly complex, and Rainbow Dash is just awesome. About all I can say for certain is that Applejack isn’t my second-favorite; who actually is, though, depends on my mood.