I can't decide. Fuck it, i'm going to bore you with some descriptions that you all already know:
Thief 2 - though thief 1 is better, thief 2 inherited and expanded on the modding community, that continues to this very day with very large and complex maps. I love the gameplay here. Ghosting is a nerve-wracking, extremely difficult gameplay. You'll only master thief after years, and then you can play the dark mod, that is harder.
Qfg 4 : the whole series is great (and you can import chars, eat shit mass effect), but this is considered the best. This is a fascinating adventure/rpg hybrid. You're not a pc gamer if you never played these at least twice, trying the different solutions.
Ultima 7 pt2 with Silver Seed : A wondrous accomplishment. So many places to explore in the wildness. The map isn't so big at first look, but every mountain, and many unreachable seas were actually used as space for dungeons. This is like a 2d gothic.
Jagged Alliance 2 : best TB squad game there is, and a quite capable little rpg lite.
Deus Ex : I put on my trenchcoat. I hear mortars in the night. I've actually completed this RT rpg/shooter without killing a single person - except indirectly in a scripted sequence. Yes, that is the kind of game it is.
MoO1 : the most additive game ever made. Utter simplicity with surprising depth. Don't be seduced by MoO2 (that is also a good game). MoO1 has the superior model.
Lost Eden: This is technically a bad game. In fact, i was unsure weather to replace this by Dune 1 that has the same appeal/merit to me, but many less flaws. But Lost Eden has that characteristic i value a little bit more, so i went with it.
Simply, both of these games have hypnotic music. Increases immersion by 300% no kidding. Same composer too. A similar effect is found on one music on bloodlines (only one, otherwise it would be here). That music is the hollywood theme.
Honorable mention (one of many i could list, but this was displaced by moo1)
Cave story : one dude alone did the best platformer of the 2000's and released it for free on the net. This is that game. Don't be deceived by the starting cave, this is like metroid on steroids. Speaking of metroid, there is a super method hack you should try if you're a pro at it: super metroid redesigned.