Scheme: honorable mentions and one distinguished title. Lots are probably missing from the honorable mentions list.
Honorable mentions:Deus Ex: nuff said above.
Diablo 1: Scared shit out of me when I first played it. It was probably Blizzard's first serious attempt in the meticulous atmosphere creating they later became famous for and was entirely successful. Brilliant nightmarish gothic gory graphics with fantastic music and a claustrophobic gameplay.
Heroes of Might And Magic III: extremely memorable and charming atmosphere, extremely diverse and brilliant music and sound effects plus a lovely extremely detailed art. Its somewhat baroque, crowded and stylized fantasy look was very stimulating to one's imagination (especially to a kid me's imagination). A good story and complex, enjoyable gameplay came with the bundle too.
May Payne 2: an outstanding incarnation of film noir in a third person shooter. One thing was the flawless adrenalin stuffed gameplay, but what raised it above peers was IMO the great effort that went into that noir atmosphere.
Half-Life 1: was much more punishing and psychologically intense than the sequel and was a huge influence on the genre as a whole. It's a shame though that since then there wasn't a very spectacular evolution in FPS games.
Counter-Strike: more a competitive sport than a video game in the classic sense. As a competitive sport it has great depth and at a time a lot of my efforts went into getting better at it. I stopped it playing years ago, however, in the end I was extremely good and up to this point I have not found anything else that can put my mind into such a highly effective, focused, meditative state that I experienced while playing. Before anybody comments here, drugs are a no-no
Portal: short and new, which would by itself warrant suspicion, but Portal is just simply a very clever and refreshing little piece. Portal had some subtle experimenting with metaphors, metafiction and deconstruction. It's a shame the game only kept these brilliant experiments in the background (so much that most players had no idea about them).
Jagged Alliance 2: it's not like Fallout or Torment that pop instantly to mind when it comes to so called "obscure, older masterpieces". They pop into mind because they are not that obscure, JA2 does not pop into mind because it is actually obscure. JA2 had a ridiculously refined tactical/strategic gameplay with tons of possibilities that were actually useful... I could write about its other virtues, but basically JA2 just got totally everything right.
Distinguished title: MorrowindThis is a game that has some obvious flaws that are so much dwarfed by its accomplishments that in my list nothing has ever come close to touching Morrowind.
Naysayers usually complain about the lifeless NPC's that are just standing around doing nothing, repetitive and simple combat and overly convoluted and loose story with fricking boring walls of texts. Well, I love those tl;dr walls of text, which is pretty much natural for someone who occasionally visits EvaGeeks. MW actually has about 1,2 times as much words as War & Peace.
Comparing MW to Bioware stuff: Bioware stuff are narrative driven, rely heavily on standard narrative and character tropes and are pretty much movie like.
In contrast, MW is entirely free-play, sandbox-type, is a sum of many diverging sub-stories and the player has an important role in setting up whatever narrative there might be. There also aren't any noteworthy companions and there is almost no nauseating romanticism and emotianality that tend to permeate JRPGs or even Bioware stuff. You've only got a huge world and are free to do whatever you want.
Typically MW seems bland compared to those two above mentioned types. However, MW has a literary, cultural and philosophical richness that makes other RPG's seem bland, maudlin and primitive. You just have to delve a bit more deeply into it.
Additionally, MW managed to sustain a hyperactive and buzzing official forum for an unprecedented 7+ years, mainly because of players who have so far created tens of thousands of mods and over the years and retextured and reconfigured the whole game many times. They even wrote a new extension to the original graphical engine and modded the game ~ to Oblivion graphical levels. Besides modding players have gone to great lengths creating Encyclopedias, databases, literary and historical analyses, etc. based on the game. MW discussion and analysis, while somewhat smaller than NGE discussion & analysis, is still a damned huge amorphous thing.
MW discussion has a unique flavor to it for the reason MW's world and lore is pretty much original and unconventional among fantasy settings. It has a certain schizophrenic vibe to it, maybe because the ingame world's complexity, vagueness and ambiguity is much closer to what's typical in the real world than in other fictional worlds.