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Pichu, Pikachu, Mudkip, Celebi, Jirachi, Deoxys, Dialga, Lickilicky (only because of the name), Uxie, Mesprit, Azelf (although each one of them was a pain in the ass to catch), Mew, and Mewtwo.
Red missingno! It may not strictly be a real pokemon, but it has a name, types, attacks, everything real pokemon have but a sprite and a real place in the game. Missingno will always be my favourite!
If i have to choose real pokmeon, i'd go for nidoking. Just cos it looks awesome. Closely followed by aggron, tyranitar, exploud...