My favorite Pokémon are . . .
Pikachu ~ Yeah, while I played several of the games, the only one I really played for an extended period of times was Pokémon Silver, and the others I played until the first gym leader until I got bored or in the case of Pokémon Yellow, screwed myself. Therefore, my knowledge of Pokémon and what immediately pops into my mind (excluding Smash games) is the anime. Particularly the first five or six seasons which may not sound impressive considering the shows got near twenty but I still sat through around two hundred episodes. With that stated, Pikachu being one of my favorite really can't be all that surprising.
Mewtwo, Meowth, Charmander/Charizrd, Squirtle, Entei & Growlie/Growlithe's ~ Again most of these should be relatively obvious if you're familiar with the anime. I'll only bother to clarify for Entei, which is because the third movie was easily my favorite of the whole bunch (that I've seen, which is like the first four then two randomly from later in the series).
Hypno ~ Entirely because of the creepypasta Hypno's Lullaby (which actually has some backing in the official games, as the video shows). . .
Pidgey (and all evolution's), Cyndaquil (and all evolution's) and Totodile (and all evolution's except Croconaw) ~ This one is obviously because of the Pokémon Silver game and not the anime.