Ok, I will try and make a top 20 list, but not in any particular order as I think these innovative games are all important in some aspect. Note, I have taken cues from this thread aswell:

1: Dune - first real RTS

2: Wolfenstein 3D - Hello shooters

3: The legend of Zelda - Open world exploring was done first here people!

4: Super Mario 64 - 3D done right

5: Pong - Goooooooood morning videogaming!

6: Populous - the true God-Game.

7: GoldenEye - Console FPS IS possible! with local Multi even!

8: Metal Gear Solid - the true father of stealth

9: Final Fantasy 4 - First JRPG to get everything right.

10: Wii Sports - I tend to be averse to too recent games in these sort of lists but motion controls seem to be the future and this game prooved that it is true.

11: Space Invaders - The start of the Shoot m up

12: Tetris - The first puzzle game, still played to this day.

13: Ultima online - This is the grandfather that occasionally smacks Word of Warcraft on it's head with a cane.

14: Quake - modding, online shootfests... still going on today!

15: GTA 3 - The first open world 3D game. I don't like it so much but it get's props for that.

16: Super Mario Bros - How long had we been stuck in 2D side-scrolling adventures up until SM64 was released?

17: Kung-Fu - The first one on one fighter, (though SF2 will always be more fun)

18: Shenmue - Engrossing story, unique setting and pacing... and let's not forget the - PRESS A TO DUCK NOW!! (Quick time event)

19: KoTor - If they can place Bioshock on the list for making right or wrong choices then KoTOR is far more deserving. Aswell as innovating in other fields.

20: The Ocarina of Time - Automatic jumping, Z-targeting, engrossing story and the first 3D adventure.

Games that just fell out of it in my humble opinion:

Wii Fit, Half Life, Mario Kart, Chrono Trigger, Micro-Machines, Alone in the Dark, Pokemon and Maniac Mansion

psst...look at #6.