My overall end all favorite Pokemon is:
Pidgeot: My favorite animal is a Falcon and Pidgeot bares a striking resemblance, so once I saw it, I knew it would always be a favorite.
Other favorites include:
Arcanine: I love dogs, and I love fire types. Plus, he just looks like such a regal Pokemon, demanding and commanding respect.
Arbok: Snakes are cool and I enjoy poison type Pokemon. Plus, I've always been a fan of Team Rocket.
Nidoking: Funny story about him. The first booster pack I bought when I was younger for the TCG, had a holographic Nidoking sitting right on top. It was both my first holographic and first Pokemon card, so I naturally fell in love with it. I still have that card today in mint condition.
Hitmonchan: Been a huge fan of martial arts for years. Also, being a huge Jackie Chan fan, I immediately loved Hitmonchan after learning that he was named for Jackie Chan. Though also a fan of Bruce Lee, I've always preferred using my hands to legs in sparring/fighting/combat.
Raichu: To be brutally and very honest, I've always hated Pikachu. I never understood the fad or the rage about him, but I have always loved Raichu, and it started out of hate for Pikachu. I still remember the Pokemon episode where they considered evolving Pikachu into Raichu to stand a better chance, and to this day, I wish they would have. So where it was once just because I hated Pikachu, I grew to love Raichu.
So there you have it, conincidentally, my favorite Pokemon is also my favorite lineup that I try to use in every Pokemon game and enjoy using the most. Never be good from a competitive standpoint, but it'll always be a favorite.
Also, just another little FYI, notice they are all from the original list of Pokemon. While there are some cool and good Pokemon in Generations II and onward, I"ve always liked and preferred first generation Pokemon over the others.
And just to cover the spectrum, I hate all grass Pokemon. So there you have it, my favorite, and my hated. All wrapped up in one.