My "Top 10" consists of a number 1 position and nine others tied for the number 2 spot. I can't really arrange the other nine in any order of preference.
1. Charmander
2. Pikachu
2. Cyndaquil
2. Mudkip
2. Quilava
2. Lapras
2. Moltres
2. Latias
2. Espeon
2. Vileplume
Charmander - My favourite of the Kanto starters, my favourite of the fire-types, and my favourite overall. I've loved this Pokemon ever since I first saw it in the anime. For some reason, I find its evolutions average at most, preference-wise, anyway.
Pikachu - Again, a real classic. I always train a Pikachu in my Red and Fire Red versions.
Cyndaquil - My favourite of the Johto starters. Plus, it's super-adorable.
Quilava - I like Quilava about the same as Cyndaquil. They're both super-adorable.
Lapras - I've trained Lapras since the days of good old Red and Blue, and I've always found it to be an awesome battler.
Moltres - I like fire Pokemon in general, but there was something about Moltres that really made me like it. Maybe it's the whole phoenix-resembling thing. I'm not entirely sure.
Latias - When I was first introduced to the Hoenn generation games, there were very few Pokemon in that generation that I didn't strongly dislike. Latias was one of these very few Pokemon. The others, I believe, were Combusken, Mudkip and Latios. I find it very cool how Latias is legendary and still has a gender.
Mudkip - See the first three sentences of Latias's description, but replace "Latias" with "Mudkip". I kind of got attached to Mudkip after choosing it as my starter when I first played Emerald.
Espeon - I started liking this Pokemon after using it on my rental team in Pokemon Stadium 2. After playing that game, I just had to raise one in my Crystal version.
Vileplume - Another classic. I've trained this Pokemon ever since the days of good old Red and Blue. It was a Red Version exclusive back in the Red/Blue days (I think it's also exclusive to Fire Red... when speaking only of the Fire Red and Leaf Green games, anyway...).