I have never had a level 100 pokemon. I never saw the point. The closest I have ecer gotten was a level 74 rayquaza in Emerald. I have also caught Pokemon over level 100 on my younger brothers blue version but I don't think that counts.
It was my Feraligatr in my first Crystal game. But since I killed Suicune in that game, I restarted, though I transferred Feraligatr and many other Pokemon I didn't want to lose onto my sister's Silver. In my current Crystal, Feraligatr is on lvl. 60+.