Gengar, for one. My all time favourite Pokémon. I grew up with it, I loved its appearances in the anime, and I love its personality.
Hmm... Either Ampharos, Umbreon, Lanturn, or Rayquaza. All Pokémon that I met later on in the games, that I've grown attached to. I'd give the nod to Rayquaza, though. My favourite legendary Pokémon, such a majestic beast.