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Charizard in Diamond. Originally came from my FireRed, where a friend raised it to Level 88 though. So the first real 100 I had was the Dragonite that started out as a level 16 Dragonair. I tell ya, that thing was hell to train.
Both went from Diamond through Platinum and are now in my White version.
I had three level 100's on my late Silver cartridge. They are the only three level 100's I have ever had. They were a Pigeot(which had been traded over with several other of my good pokemon from my yellow Cartridge. That pigeot was the first pokemon I had ever caught), a Dragonite, and a Furret. I can not remember which one reach level 100 first however.
the red guyrados from silver version (with out cheating) i cheated to get a lvl 100 lugia and dragonite, but i trained guyrados fair and square, then used him in pokemon stadium 2.
second was a Mr Mime from Emerald and that Mr Mime is still with me today on my White :P it was 70ish when it left Emerald and was 97 a few days ago when it hit white and now its 100
I think my first one was either Charizard (Blue/Red) or Typhlosion (Silver). My Silver died a long time ago, and I think I restarted both my Blue and Red versions a while ago too.