(Excluding games that are VN's or have VN elements, because it's otherwise Virtue's Last Reward, which is a VN)
My favorite game of all time: Portal 2
Why? An engaging story, wonderful gameplay, beautiful setting. Flawless characters which made me enjoy the story immensely even though I was spoiled even my first time around.
The gameplay is not as minimal as Portal, but still feels fresh and diverse. There's now user level support, so one can pretty much test for an indefinite amount of time.
And I still haven't completed co-op...
Runner-ups (no particular order):
System Shock 2
An absolute masterpiece on survival horror and FPS/RPG in the gameplay department. You can play through it at least three times (as Marine, Navy and OSA) which will all be incredibly different experiences. Throw in a spaceship, logs so detailed that the fanbase has pinpointed the identities of at least half of the corpses found in the whole game, mods as long and diverse as the game (just google System Shock Infinite), a thought-provoking story, a long campaign...
This game is borderline flawless.
Bioshock
The story and tale of Rapture, like its spiritual predecessor System Shock 2, is beautifully woven. The gameplay, while not satisfying on paper, is surprisingly addictive. The story doesn't stand up to Infinite's, but the lore is beautiful in its own right. Most gameplay elements have a place in the story, though your decisions don't do much. There are quite a lot of ways you can play, and the level design is incredibly beautiful.
Dead Space
Seeing a pattern? Yes, I love "get the fucking hell out of this derelict place which is scary as hell but also filled with interesting things to the brim" games. The upgrade system, the lack of a HUD, just how fun it is... Dead Space is another series I love (the second and third games kind of suck with the story though, and Isaac isn't likable in 2 or 3 at all) but it's beneath the other three masterpieces in this list.
I'm kind of a video game hipster, many games (especially open world ones) are games I find very boring: Skyrim, GTA, CoD, etc.