Team Fortress 2 (the best game ever): link
Gang Garrison 2 (the 8bit de-make of Team Fortress 2): link
Narbacular Drop (where Portal's portals came from): link
Tag: The Power of Paint (where portal 2's gel puzzles came from): link
Quake Live (browser-based version of Quake 3 that we all know about): link
Wolfenstein - Enemy Territory (the multiplayer expansion for Return to Castle Wolfenstein that ended up being released for free on it's own): link
Battlefield Heroes (EA's free to play FPS, it's more cartoony than the other Battlefield games & relies a bit too much on micro-transactions): link
Grand Theft Auto: link
Grand Theft Auto 2: link
Wild Metal: link
Command & Conquer: Tiberian Dawn: disc 1, disc 2 & how to get it working
Command & Conquer: Tiberian Sun ( W/Firestorm): download & how to get it working
Command & Conquer: Red Alert: disc 1, disc 2 & how to get it working
Minecraft (the free version is missing a lot of stuff from the version you can buy, but you can still get your build on): link
That's it for now, but i'll update the thread on a regular basis.
If you know of any others that are legitimately free, let me know & i'll update the list.