My turn! Let's see:
1. Applejack: To tell you the truth, I have no idea why she is my fave pony; something about her seemed so adorable, right from the start, but I can't quite put my finger (or hoof XD) on it; can it be the fact that her element is honesty? or that she takes great care in making sure her friends are happy? or that Applebuck Season, on of my faves, was so early in the show? or that she has the same eye color as me? I dunno, maybe it's all of these reasons, she's still my fave pony from the show, no doubt about it XD
2 Rarity: They really outdone themselves when they created her, she is an unbelievably complex character; I remember reading somewhere a short review on her and it simply turned my perspective around, for the better. Don't get me wrong, I liked her before, but it was then when I realized just how perfect her character was and that we always find out new stuff about her with every episode she's in
3 Pinkie Pie: well...she's Pinkie Pie, need I say more? XD
4 Twilight: she's in many ways the protagonist of the show and many times, we see the situations through her eyes; also, in the first episodes, she's seen more or less as "the new pony" by Ponyville's residents; it was really fansinating to see how she was able to make so many new friends in such a short period of time, quickly getting over her "friendship isn't my thing" approach
5 Fluttershy: please don't think that I don't like her or anything, I like all the mane 6 chars, no question about it; Fluttershy is a really great pony with lots of wonderful qualities about her, not least of which that she cares about all living creatures so much; the only downside is that I don't think many ponies are aware of her qualities due to her being too shy to show them
6 Rainbow Dash: again, please don't think that I dislike her or that I have something about pegasi (if I'd be able to choose what I wanted to be, I'd be a pegasus, since I'd love to fly, but that's besides the point XD) she's a really great friend to have, especially since loyalty is her thing; yup, as the fellow pony above me stated, she does boast too much sometimes, but you know what? that's what makes her all the more likeable XD again, don't consider number 6 to be the pony I like the least; truth be told, numbers 4 to 6 are pretty much on the same level XD