These are only the games that I can quickly recall off the top of my head. I know that there are several others that I am forgetting (edit: moved Magic Realm down below since I found the name).
d20 Modern
GURPS: various genres
Hero System 4e: various non- supers genres (I listed Champions 4e separately below)
Savage Worlds
7th Sea 1e
Ars Magica 3e
Dungeons & Dragons: Original, Holmes, B/X, 1e, 2e, 3
Elric/Stormbringer
Legend of the 5 Rings 1e
(edit): Magic Realm: I have seen this described separately as an rpg and a board game. It was introduced to me as the former, but feels to me like the latter (or an indie type game))
Middle Earth Role Playing (ICE)
Rolemaster 1e, 2e, RMSS
Warhamer Fantasy 1e
Boot HIll 2e
Bond 007
Spycraft 1e
Top Secret
Top Secret S.I.
Call of Cthulhu
Ghostbusters
oWorld of Darkness Mage: 1e, Revised
oWorld of Darkesss Vampire 1e, Revised
oWorld of Darkness:Werewolf: 1e, Revised
Champions: 3e, 4e
DC Heroes (Mayfair): 1e, 2e
Living Legends (playtested the version that became the game, iirc it switched in playtest from what is now "Advanced" V&V)
Marvel Superheroes (TSR): Basic, Advanced
Mutants and Masterminds 1e, 2e
Villains & Vigilantes, 1e, Revised, Advanced/LIving Legends
Teenage Mutants & Other Strangeness
Cyberpunk: 2013, 2020
Gamma World 1e
Mekton
Robotech (Palladium)
Shadowrun 1e
Spacemaster
Star Frontiers
Star Trek (Fasa)
Star Wars (WEG)
Traveler
Twilight 2000
Made Men
Toon
Edit: I still have so many games on my list to try: Apocalypse Prevention Inc, Atomic Highway, Barbarians of Lemuria, Big Eyes Small Mouth 3e (or 4e), Cinematic Unisytem (Angel, Buffy), Classic Unisystem (Conspiracy X, Terra Primate, Witchcraft), Cortex Classic, Cortex Plus games (Firefly, Marvel Heroic, Smallville), Honor + Intrigue, Icons: Assembled, BASH: UE, Supers: Revised, Cartoon Action Hour Season 3, Meddling Kids, H.P. Lovecraft Academy, Ninja Crusade 2e, Pip System, Tiny Dungeons 2e, Adventurers! (Adventurers Acadaemy, Gothica Kung Fu Adventurers!), Mythic d6, Coyote Trail, EarthAD2, Ubiquity System (Leagues of Adventurers, Leagues of Cthulhu, Leagues of Gothic Horror, Hollow Earth Expedition,) Kids on Bikes, vs. Stranger Stuff