GameFAQs released a fun little tool that has you vote between two games repeatedly and then gives you a list of your favorite all-time games based on your answers. Obviously it's not perfect since it doesn't list every game ever, but it does a pretty good job of hitting most of the major titles.
http://slimedrippings.tumblr.com/gamefaqssort
My list, according to this:
1. Ocarina of Time
2. Half-Life 2
3. Super Mario 64
4. Portal 2
5. Super Mario Bros 3
6. Team Fortress 2
7. Metal Gear Solid 3
8. Metal Gear Solid
9. The Witcher 3
10. Deus Ex
11. Fallout 3
12. Final Fantasy Tactics
13. Morrowind
14. Half-Life
15. Chrono Trigger
16. Star Wars: KOTOR
17. GoldenEye 007
18. Portal
19. Red Dead Redemption
20. BioShock
I'd probably change the order of some of those around, but the top five pretty much nailed five of my favorite all-time games, and the rest of the list is pretty spot on. It goes on to list over 100 games, but I didn't feel like typing all of that out.
I would say the main issue with the tool is that there's no option for "haven't played that," which means you're stuck voting until you get two games you haven't played and saying you feel the same about them. There are games I haven't played, like Journey, that are somehow higher ranked than games I have played and really liked, such as Last of Us, which doesn't make a lot of sense.
Still, a fun thing to dick around with for ten minutes.