0 AD, RTS, similar to Age of Empires
Barkley, Shut Up and Jam
Battle of Wesnoth, turn-based strategy
Battleships Forever, RTS
Bubsy 3D: Bubsy Visits James Turrell Retrospective
Cannonball, open-source OutRun port
Cave Story, you probably know this game.
Classic Game, like ???
Dongland Repainted, I don't even know anymo
Duck Marines, Chu Chu Rocket clone, open-source
Dungeon Crawl Stone Soup, roguelike, 'nuff said >:D
Enviro-Bear 2000, lol
Flight Gear, flight simulator
Freeciv, Civilisation clone, open source
Four Winds Fantasy DX
Ghosts of Aliens
Hedgewars, Worms clone, open-source
I Wanna Be The Guy, oof
illegal crime game
Irusu Syndrome, Japanese puzzle game, English patch
Jake Clover's games
Knytt, explore world, find UFO
Lisa the First, I really need to play the Lisa series aaaah
Lost in the Static, " free exploration-oriented platform/jumping game"
M dot Strange's games
Mari0, Super Mario Bros., but with some Portal flavours
Mega Man 8-bit Deathmatch, FPS Mega Man game
Minetest, Minecraft clone, open-source
Nethack, 'nother roguelike, 'nuff said >:D
Openarena, FPS based on idTech3, open-source
Openra, Command and Conquer clone, open-source
Openttd, Transport Tycoon Deluxe clone, open-source
Painted Tomb, "A story of companionship, betrayal, misguided inclinations toward revenge and ultimately the road to something else (although the pain and memory of misgivings may linger.)"
Photopia, interesting interactive fiction
Pirate Kart V, and pretty much the entirity of Glorious Trainwrecks
Sonic Robo Blast 2, Sonic on Doom engine. Surprisingly awesome
Super Tux Kart, kart racer with the linux mascot
Tiny Fragments, neat puzzle game
thecatamites' games, some of these are not free mind you, but most are. Space Funeral is their most known game, but is highly recommended.
TUMIKI Fighters, pastel shmup
UFO Alien Invasion, XCOM clone, open-source
The Underground Explorer
Warning Forever, bossrush shmup
Which, short horror game
The White Chamber, point 'n' click sci-fi horror
Xocotl: God of Stars
Xonotic, FPS similar to Quake and Unreal Tournament, open-source
Yume Nikki, does it need an introduction? It's an amazing experience!
Zero-K, RTS with robots