This is a (mostly complete) list of the Pokémon I've trained to level 100. If I trained more than one of the same in a game, it's probably because I decided its stats or moveset sucked.
In bold is the primary team I used in that particular game. I think anyway, I can't remember all of them exactly as they were without going back and looking.
Yellow (24 total): Venusaur, Charizard, Blastoise, Pidgeot, Raichu, Sandslash, Clefable, Vileplume, Arcanine (x2), Poliwrath (x2), Alakazam, Magneton, Hypno, Exeggutor, Gyarados (x2), Lapras, Vaporeon, Zapdos, Dragonite (x2), Mewtwo
Gold (12 total): Raichu, Arcanine (x2), Exeggutor, Gyarados, Dragonite, Ampharos, Espeon, Umbreon, Tyranitar, Lugia, Ho-oh
Crystal (10 total): Arcanine, Gyarados, Dragonite, Ampharos, Espeon, Kingdra, Raikou, Entei, Suicune, Tyranitar
Emerald (11 total): Arcanine, Gyarados, Dragonite, Ampharos, Tyranitar, Aggron, Milotic, Metagross, Kyogre, Groudon, Rayquaza
FireRed (1 total): Mewtwo
Diamond (8 total): Arcanine, Gyarados, Dragonite, Tyranitar, Metagross, Electivire, Dialga, Giratina
Black (10 total): Raichu, Arcanine (x3), Gyarados, Dragonite, Tyranitar, Gardevoir, Lucario, Hydreigon
Black 2 (13 total): Arcanine (x2), Cloyster, Gyarados, Dragonite, Tyranitar, Metagross, Luxray, Garchomp, Lucario, Electivire, Darmanitan, Zoroark
So 89 total Pokémon trained to level 100 if I counted correctly. Including 12 Arcanine! I've been super busy in Black 2 training stuff up. I've been playing it nonstop since it released!
If I plan on using a Pokémon on one of my main teams on a new game, I always breed a new one even if I already have a good one. I attempt to get better IVs each time, though it's not usually much use trying these days. It also gives me another chance at adding another moveset, nature, or EV spread to my list of battle options.
My Crystal and Black 1/Black 2 games are still home to most of these Pokémon. A lot of them have fond memories attached to them, which is one of the reasons I get angry when people say we shouldn't be able to transfer old Pokémon to the new games.