Man, great choices there, including a few of my all-time favorites like Half-Life, Halo and GoldenEye.
I would say my favorites have to be Doom, Doom II, Final Doom and Doom 64 (am I missing any original Doom titles?), as well as the 3 I just mentioned.
Was never really that fond for Quake. Unreal Tournament was really cool, though.
Duke Nukem 3D never really caught on with me. I liked the urban setting but I would just rather play the (in my view) superior Doom games.
Can't make a top 5 and I'm sure there's some I'm forgetting, but can't go wrong with any of these.
Good man with good tastes.
I could have wrote it with just few variations. Doom can be replaced by Ultimate Doom, Doom 64 removed (never played it). I enjoyed anyway DN3D first parts and play it pvp over modem, but even if it's MP was fun, it could not match Doom with 4 players sessions at job, all in same place. In Single Player I enjoyed Q3A but for MP UT was a rather big stuff and it won also because it was the big stuff, hence it was grabbing most players and the best players diversity, still I have only despise for those dev rippers. Q2 was the best Single Player of the Quake series and even captured back a bit of Doom mood, still no match with Doom.
Otherwise, I must confess that my top can't stick just to that, so my own, pure Single Player point of view :
1 - Doom 1&2
2 - Po'ed
3 - Selection of Doom 1&2 wads (sorry too far ago, no list)
4 - Marathon 1 (eventually 2&Infinity too)
5 - Far Cry
6 - E.Y.E Divine Cybermancy
7 - Mass Effect 3
8 - System Shock 2 (remove the close combat crap and the respawn abuse and I'll reconsider it to some 2/3 position)
9 - Far Cry 3
10 - Doom 3
And a mention for Pathway Into Darkness, Serious Sam 3 BFE, Half Life 1&2, Aliens vs Predator, Clive Barker's Jericho with QTE removed.
EDIT: I quote my top 4 is fps where you had a lot of dodging not just anticipated dodging or smart moving. If I knew 10 fps focusing on real dodging they would take all ten places.
The new old school is missing a bit in the list, it's not dodging it's focus on anticipated dodging and smart movements, Serious Sam 3 BFE is a typical example, Doom 4 I don't like is probably another example.
Otherwise there's in the list the open world focus, the linear focus, the cover focus, the RPG focus, 3 classic sub genres of modern fps and one that should become a classic.
I suspect I'm now incompatible with fps, my current last hope is New Wolfenstein. But I need come back to play it.