There's different ways you could go about this. Do you go with the games that are the best exemplars of their form? The games with the fewest flaws? The games that the largest number of people react to the most favorably?
In 2007, I
polled people at selectbutton.net for their top 25 games, and using my favorite voting system—an unnecessarily convoluted one—I compiled the following list from their answers:
25. Tetris
23.5 Ikaruga
23.5 Sonic 3 and Knuckles
22. Castlevania: Symphony of the Night
21. God Hand
20. Final Fantasy VI
19. Super Mario 64
18. The Legend of Zelda: Majora's Mask
17. Katamari Damacy
16. Cave Story
15. Planescape: Torment
14. ICO
13. Killer 7
12. Bangai-Oh
11. DOOM
10. Metal Gear Solid 3: Snake Eater
9. Deus Ex
8. Street Fighter 3: Third Strike.
7. Chrono Trigger
6. Super Metroid
5. Silent Hill 2
4. Super Mario Bros. 3
3. Earthbound
2. Shadow of the Colossus
1. Half-Life 2
(Ikaruga and Sonic 3 and Knuckles were for 23rd place.)
If I were to adapt this list for these purposes, I'd remove SF3 because its greatness comes from multiplayer, so Doom makes the top ten.
I would replace Half-Life 2 with Portal.
I'd prefer Mother 3 to Earthbound, but I feel like those two games + Chrono Trigger are interchangeable exemplars of console RPGs and I'm happy with a list that includes one of those, so let's toss the other two and scooch Bangai-Oh onto the list, as well.
As much as I
like Metal Gear games, the franchise is a hot mess and however deliberate it might be, I'm disinclined to include one on the top 10. I feel similarly for Killer 7: I like the game, I think it's a
great game, but I feel like its merits come more from a reaction to and against other games rather than through some sense of universality.
Ico is like Chrono Trigger in that I think it's great and broadly accessible, but it occupies a similar enough space to Shadow of the Colossus that I'm comfortable including only one.
The more I think about Planescape: Torment, the more I think it's overlapping with Deus Ex. I personally like Torment better, but I think Deus Ex has more universal appeal and a more coherent approach to design. Maybe just pick the one you prefer.
Cave Story's pretty good but it overlaps Super Metroid, Bangai-Oh, and Zelda games enough that I'm starting to doubt how best to represent this constellation of gametypes. Bangai-Oh is mechanically excellent, but I'm starting to feel like single-player games really should use your mechanical interactions to say something or tell a story, so my preference is to leave in Super Metroid, leave out Bangai-Oh and Cave Story, include a Zelda game for its mechanical distance from Metroid and its melodrama—while I'd accept Majora's Mask or Adventures of Link, I actually think Link's Awakening is the strongest candidate here.
Finally, I feel like Super Mario Bros. 3 and Katamari Damacy are perfectly fine right where they are.
So, at this moment at least, my final list probably looks something like this:
10. The Legend of Zelda: Link's Awakening
9. Katamari Damacy
8. Planescape: Torment
7. DOOM
6. Super Metroid
5. Silent Hill 2
4. Super Mario Brothers 3
3. Mother 3
2. Shadow of the Colossus
1. Portal
(I really should just play Doom already.)