My first two are clear-cut, but after that, I don't really have a ranked preference list:
1. Blastoise: My favorite Pokemon, period. It's the first Pokemon I ever saw, my original starter, and a member of many of my teams.
2. Pikachu: Pikachu seems to get a lot of hate for being "too cute" or being associated with Ash, but I've always loved it. Yes, it's cute, it seems reasonably smart in the anime at least, and it was a key member of several of my teams. And when my Yellow one learned Surf through Stadium, it became even better.
Kanto probably has my favorite Pokemon overall, so there are a lot of Pokemon I like a lot. I'll just name a few that rank fairly highly (in Pokedex-ish order):
-Bulbasaur line: My least favorite Kanto starters, but still high among my starter preferences overall.
-Charmander line: Like Bulbasaur, didn't use Charmander and its evolutions much in my first Red run (since I was using Blastoise), but I traded one in later on, and have used them on other games. Charizard might come in at #3 on my overall list.
-The rest of the Squirtle line: Can't leave them out.
-Nidoking: Versatile, and I love his shiny. A slightly more recent favorite.
-Arcanine: Not sure why. I guess I like the way it looks.
-Alakazam: Just a great Pokemon.
-Gengar: I had a very hard time with the whole link trade thing at first (no one I knew bothered), but I used the rental Gengar in Stadium, and it became a Pokemon I liked a lot. It's held up very well competitively over the years, too, which is a plus.
-Jolteon: I happened to evolve my Eevee into this my first run, and though I didn't use it much then, it's one of my favorite Eeveelutions.
-Aerodactyl: My favorite fossil.
-Snorlax: Useful in battle, and it even gets its own field object and special encounter in a lot of games.
-Zapdos: My favorite of the legendary birds.
-Mewtwo: Amazingly powerful in gen I, and the culmination of my Red Version experience. I remember tossing my first Master Ball at it while thinking up not-very-creative nicknames (I think I went with "Two" for the first one). I'm still a little sad that Mewtwo has fallen since its glory days, but it's still a great Pokemon.
It's interesting that there aren't more water types, as water is my favorite type, but I guess I didn't use other water types too much because I was always using Blastoise. Lapras and Starmie could use honorable mentions, though.