Gen 1: Hard to pick. Mewtwo is badass, Arcanine is the best doggy ever, Ninetales is pure beauty, Eevee and Jolteon are killer-dorable, Beedrill is positively insane, Gyarados and Alakazam wreck shit, Pikachu... shut up I like Pikachu, and Missingn*&@$*&@$(*&!. But, the one that I would call my "favorite" is Articuno. The Ice bird exemplifies grace and beauty, and has an Ice Beam that destroys entire Elite Fours.
Gen 2: Umbreon. Sure, it's not all that great competitively, but this was the tankiest little sucker I ever had, plus could kill with Perish Song and Mean Look. Gen 2 has most of my all-time favorite pokemon as well. Lanturn is an oddball but plays solid support, Scizor, Heracross, and Tyranitar just wreck more shit, though T-tar wasn't that great before the physical/special split (dark was special only). Espeon is another killer-dorable Eeveelusion. Houndoom is pure badass, and the only special-oriented Dark type at the time. Sneasel was exactly what one might expect a Dark/Ice type to be, and got radically better with the special split, letting him finally use his physical attacking stats.
Gen 3: Blaziken, not close. Yes, I liked Blaziken "before it was cool". Powerful attacking stats and Bulk Up standard, letting me one-shot the Elite Four dragon trainer's Salamence with Double Kick. Honorable mentions go to Absol, Gardevior, Tropius, Sharpedo, Metagross, and Groudon.
Gen 4: Palkia. Palkia's a pretty, badass, legendary Godzilla-thing, enough said. Pachirisu gets honorable mention for being just so damn cute... and the only gen 4 pokemon I can think off off-hand, which says a lot. *looks it up* Aha, I remember now! Honorable mentions: Empoleon, Staraptor, Lucario, Gabite (I don't know, I like Gabite more than Garchomp), Yanmega, and Electivire.
Gen 5: Mienshao. Shut up, it's pretty. Plus it's a badass Fighting type that can abuse the crap out of Aura Sphere and Hi Jump Kick. Honorable Mentions go to: Golurk, Hydreigon, Sigilyph, and Joltik and Deerling, who are damned adorable.
Gen 6: Talonflame. You guys... just get a Talonflame. Seriously. You won't regret it. One must experience how badass this thing is. Who would have thought the Gen 6 version of Pidgey would evolve into a meta-defining staple? Honorable Mentions go to: Chesnaught, Aegislash, Clauncher/Clawitzer, Goodra. I'm not counting Megas as separate pokemon, though if I did, MegaBlastoise and MegaMawhile get honorable mentions too.