Here's my top 10. What are yours? Let's not count extreme genre hybrids like Mass Effect and modern Fallout and Deus Ex series and Underhell in here.
1) S.T.A.L.K.E.R. Shadow of Chernobyl - Setting/atmosphere, open ended, A-Life, mission design/variety, gameplay, story, mods.
2) S.T.A.L.K.E.R. Call of Pripyat - Setting/atmosphere although not as special as SoC here, nice gameplay improvements, mods. I love the survival aspect with Misery 2.
3) S.T.A.L.K.E.R. Clear Sky - Setting/atmosphere on point again although not quite SoC level, some very interesting dialogue at least early on, impressive A-Life in faction wars, mods.
4) Metro 2033 Redux - Atmosphere, storytelling, survival gameplay, I love it all.
5) Metro: Last Light - For the same reasons as 2033, and I love the more detailed level design and stealth.
6) Cryostasis: Sleep of Reason - I think this counts since the horror is more thematic than anything. Gameplay is all shooting plus holding a button/key over heat sources. Story and atmosphere are the main reason I rate this so high.
7) Half-Life 2 - Primarily with Cinematic Mod 2013. Wouldn't rank this high without it, as it needs it to become an amazing atmospheric experience. Good gameplay diversity.
9) Crysis - Also for Power Struggle.
10) ArmA 3 - So much to do and create, I love the simulation gameplay aspects.
Honorable mentions: ArmA 2, Rainbow Six 3: Gold, Natural Selection 2, Black Mesa.
Here is Enad's top 10 for reference:
1) Spec Ops: The Line
2) The Bureau: XCOM Declassified
3) ArmA 3
4) ArmA 2
5) Call of Duty 4: Modern Warfare
6) Battlefield: Bad Company 2
7) Call of Duty: Modern Warfare 2
8) Metro: Last Light
9) Metro 2033 Redux
10) Battlefield 1