This is always a tough one :3
I figured I'd post a small list as well. Here's my top 20:
1. Arcanine- A great fire Pokemon. Looks like a beast, fights like a beast. He's a pretty well rounded guy.
2. Gyarados- Who doesn't like this guy? Like Arcanine, he's epic- stat wise and appearance wise.
3. Eevee/Eeveelutions- My favorite evolutionary line, the eevees are pretty useful Pokemon in any game- and look awesome.
4. Dragonite- He's the best of the best. My favorite monster of the first generation.
5. Typhlosion- My favorite fire starter line, with pretty nice stats.
6. Ampharos- My favorite electric Pokemon! Currently my Pokemon XD powerhouse!
7. Lugia & Ho-Oh- One of the coolest pairs legendaries you'll ever come across.
8. Blaziken- Another epic fire starter line.
9. Zigzagoon- I could never put my finger on it, but I've always loved this guy.
10. Ludicolo- He's been my favorite monster of the third generation from the start appearance wise.
11. Shiftry- I love this guy, and his entire line.
12. Gardevoir/Gallade- My favorite psychic Pokemon line, who doesn't love this elegant duo?
13. Aggron- This guy is a straight up tank- 180 defense stat!
14. Grumpig- Another long time favorite of mine.
15. Absol- I love everything about this disastrous Pokemon.
16. Walrein- He's been a team member of mine since Emerald!
17. Salamence- This guy looks great and fights great.
18. Luxray- Another one of my favorite electric Pokemon!
19. Lucario- Everything about this guy is fantastic- what's not to like about him?
20. Rhyperior- My favorite of the 4th Gen!
Woah, I got pretty carried away D:
That's not even including the 5th generation!
I suppose of all of these Pokemon, I'd have to choose either Ampharos, Walrein, or Lucario as my favorite.