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It's very hard to narrow it down to one, as I feel my top 5 are all loved equally.
Gengar
Raichu
Luxray
Arbok
Emolga
Luxray and Gengar have been my complete companions - It's the emotional attachment of EV training my Gengar to level 100 and raising my Luxray (which isn't fully EV trained) since I picked up my DS Lite and Platinum, training him since a Shinx.
I just love Raichu's design and thought he was one of the coolest Gen I Pokémon (both in terms of design and functionality) and watching him and Lt. Surge destroy everyone in town was awesome.
As for Arbok, I really like snakes. And love Jesse. I've just never gotten to train one properly, I think I may do that soon.
Mawile is very close to my top 5.