Ooh, so hard to decide! I have plenty of favourite Pokémon.
In fact, really, I like all Pokémon. Except for maybe a couple if I think about it hard enough. (Dunsparse and Spiritomb come to mind... and perhaps Vespiquen also...)
I really love Bulbasaur and its evolutions... Which is surprising, considering I've liked Bulbasaur even before I finally gave in to liking the colour green. Pikachu and its evolution/devolution are of course some of my favourites too, on the same level as Marill and its evolution/devolution. (If I were a Pokémon, I'd either be a Marill or a Pikachu!)
Unfortunately I can't really pick out many others in the second generation... because I never really played the games. I have a Gold cart, but it seems to be in Japanese, so I can't play it...
I warmed incredibly to Ralts, Kirlia and Gardevoir (and eventually Gallade) when I discovered them, because they're so elegant and beautiful, to the extent of Pokemon like Goldeen, Dewgong and Suicune. I especially like male Gardevoirs, because I'm quirky like that. ;D
Out of the brand-new Pokémon, I haven't really had chance to warm to many of them, but one that instantly caught my affections was Shinx and its evolutions. I have waited so long for a lion Pokémon! (Now we just need wolves... yeeees...)