I had a lv. 100 Mewtwo from one of my earlier Blue save files.....it was lost when my Crystal save file erased itself....I can get it again, though. I also have a lv. 90-something Mew on my Yellow version. My friend cloned it and traded it to me.
....I've had other lvl. 100 Pokemon, like my Latias on Pearl, my Lugia on Crystal...those are the only ones I can remember.
My Absol on Pearl is only a few levels away from reaching 100. When I reorganized my team, I was originally going to try and get an Absol with Super Luck, but since the one I had was already at lvl. 70-something, I decided to leave it as is. Thank goodness for the Razor Claw! =D