Crystal has all of my good pkmn on it, so yeah...I was a second-gen freak, so I have a lot of good pkmn on there, too bad second-gen was linked to first-gen with the candy code, or else they probably would have linked second-gen to the further games...
My Gold, Sapphire (deleted), and Red Versions have my best Pokemon. The first game I get for each generation usually does since I spend most time on them.
Um, most likely Leaf Green. It has the most Pokémon, all with levels above 60, so I'd say that. Plus, currrently, this is the only file with my Marshtomp on it. ^_^
Blue version! I have a couple level 100 teams on it, and I traded my high-level pokémon to it from Yellow to before I restarted on that cartridge. So... yeah. I spent so much time playing Blue...
Emerald, though the Level 100s there were trained on Ruby. All of my good Pokemon are still at Level 50, though, for the Battle Frontier. (I'm too lazy to train all of them up to 100 now.)
I also have a team of Level 100s on Blue, but their movesets are laughable.