Most of us gave already taken a gander at the Friend Code section and posted up our favorites, but we can have more of an *in-depth* discussion here, I should think. My favorite Pokemon are Weavile, Staraptor, and Typhlosion, though I like each for completely different reasons.
I like Weavile because two of my favorite Pokemon characters have it. Silver from Pokemon Special (Pokemon Adventures) has a Weavile, and Paul/Shinji from the Pokemon anime has a Weavile. Not to mention, Dark is one of my favorite types, and so is Ice... so what better is a Pokemon that has BOTH types in one??
Staraptor just looks awesome. Its feathers sort of resemble that typical "emo" haircut and its color scheme is very cool (black and white with a side of red). Besides, it has Brave Bird and Close Combat, plus Intimidate. That, mixed with its Pokedex entry, gives it a feeling of toughness and coolness.
Typhlosion has been a childhood favorite. Admittedly, I never liked the RBGY starters (Charizard, Blastoise, Venusaur)... but when Johto came along, I had serious trouble picking my favorite. Meganium just looks great, it has that whole dinosaur but flowery feel. Feraligatr is awesome, who doesn't want an alligator that looks like that? But Typhlosion had this extra "awesome" feel to it, and for some reason, I've been attached to it since.
My favorite generation so far is Johto. After that, I like Sinnoh, then I like Hoenn. Kanto just doesn't click with me very much....