ScrewAttack.com put together a video countdown of the top 10 FPS games of all time. I suggest you go and watch the video, but for discussion here's their list:
1. GoldenEye 007
3. Call of Duty 4: Modern Warfare
4. Wolfenstein 3D
7. Duke Nukem
8. Half-Life 2
9. Doom 3
It's a pretty solid list, although there are definitely some items I'd shift around. I don't think they're so consistent about whether this is a list of most influential games or most polished. The choice of Doom 3 over the original Doom throws it all out of whack.
I was curious how their list compared to review scores, so I put together a Metacritic query to get the top rated FPS games of all time. Collapsing to one entry per franchise, this is what you get for the top 10:
1. Perfect Dark (97)
2. Halo (97)
3. Half-Life 2 (96)
4. GoldenEye 007 (96)
5. BioShock (96)
6. Quake (94)
7. Gears of War (94)
8. Call of Duty 4: Modern Warfare (94)
9. Unreal Tournament 2004 (93)
10. Thief: The Dark Project (92)
In case you're curious, here are the rest (this is from the top 50, which only includes games with a rating of 89 or greater, collapsed by franchise):
11. Team Fortress 2 (92)
12. No One Lives Forever 2: A Spy in H.A.R.M.'s Way (91)
13. Rez (Import) (91)
14. Star Wars Jedi Knight: Dark Forces II (91)
15. Battlefield 2 (91)
16. Crysis (91)
17. Chronicles of Riddick: Escape From Butcher Bay - Developer's Cut, The (90)
18. Wolfenstein: Enemy Territory (90)
19. Einhander (90)
20. TimeSplitters 2 (90)
21. Tom Clancy's Ghost Recon Advanced Warfighter (90)
22. Metroid Prime 3: Corruption (90)
23. F.E.A.R. Combat (90)
24. Portal (90)
25. Bangai-O Spirits (90)
26. Far Cry (89)
27. Max Payne (89)
28. Descent 3 (89)
29. Duke Nukem 3D (89)
Wolfenstein 3D is too old to show up on Metacritic, which explains its absence. As is the original Doom. I didn't hit Doom 3 at all in my walk through the top 50. Turns out it was a couple pages further down, with a rating of 88.
You'll also notice that Counter-Strike isn't on the list. That's largely because the version that people are still playing is a free mod, which puts it outside the scope of Metacritic. It's successor, Counter-Strike Source, does show up, with a rating of 88. It's hard to figure out a proper rating for these mini titles. You'll notice TF2 and Portal in the list above, although technically they could be roped under The Orange Box, which is how most people played them (a title which rates at a very high 96).
Duke Nukem is further down the Metacritic list than it is on ScrewAttack's, but I'm going to have to agree with Handsome Rob on this one. Duke Nukem was pure awesomeness back in 1996. It's elusive sequel is the butt of many jokes, but when that epic trailer hit in 2001 you know were excited. Hell, it still looks like it'd be fun.
But there's one place where I think the placement of ScrewAttack's list is way off, and that's for Half-Life. The PC is the prime platform for the FPS genre, and Half-Life is the best selling FPS on that platform (although yes, Halo 3 has sold more, but just barely). But ratings and sales aside, Half-Life for me personally is definitely #1. I know I'm a little biased, but I can honestly say that I wouldn't be where I am today in life without this game.
One thing I think is a little odd about the Metacritic list is that Metroid Prime 3 shows up as a shooter but Metroid Prime (one of the highest rated games of all time with an 87) does not. Having played all three of the Prime games, I'd have to say that they all are pretty equivalent in their shooter content. The Wiimote makes it easier to look around, but the core shooting mechanic still isn't the highlight of the gameplay. But it's more of a shooter than say Portal, which does show up. Bleh, all that genre stuff gets more and more muddled every day.
So what about my list? Ugh, that's hard. I think I can tell you this much:
I missed the whole Perfect Dark and GoldenEye thing. I was off in PC land playing too much Starcraft to care about early console shooters. Funny thing, Starcraft only averages a Metacritic score of 88, which shows you about how much weight to put in subtle score differences.
One of these days I'm going to crack down and list all the games I've ever played, autobiographically (High Fidelity style). Maybe then I'll feel like I've done the proper amount of introspection to present you with a solid top 10 list.