Don't have just one favorite, but I'll go for some of my top favorites.
The nidorans, and nidorina - I forget what it was exactly that made me start liking the nidorans, but I think part of it was me feeling pity over how they didn't seem to be as popular as other pokemon (from what I saw). Whatever it was, they soon turned into one of my favorite pokemon, with me liking the male a bit more at first. I started liking the female line more, though, after I saw the crystal version animation for the nidoran female and saw the way her whiskers twitched...eee....
Anyways, I find the nidorans to be cute, and nidorina to be rather pretty.
Furret - it was one of those "love at first sight" things, I guess. O_o When the new pokemon for gold and silver were just being shown on websites, I saw furret...and thought that it was one of the most adorable things I've ever seen.
Latias - similar story as above, though not quite. It's not just the cuteness factor for her, but also that I find her (and latios') design to be rather unique for a dragon. And the sounds she made in the fifth movie...oh man. I loved that. I think another reason for me liking her is that she exhibits qualities of not just a dragon, but also a bird, and I love both of those.
Quilava and Typhlosion - I always thought they were rather neat to begin with. I forget why they've become a top favorite of mine, though. n_n;;;