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× has Dungeon Hack, which is basically a roguelike Eye of the Beholder (for new kids, think of it as a roguelike Legend of Grimrock). I have spent waaay too much time on that one back in the day.
I just want to say thank you for this thread. I looked at all the suggestions and made a few purchases as a result.

There's little I can add but may I put forward the following recommendations.

Tron 2.0
An FPS that takes place inside a computer with atmosphere and environments to match.

The Moment of Silence
A point and click adventure game. A great story and interesting puzzles. One of the few games that I loved so much I bought on steam (which I usually try and avoid at all costs).

Another point and click adventure. Comic style artwork, cool dialog. tough puzzles.

The Dig
An old Lucas Arts adventure game with dated graphics. An excellent example of a scifi adventure game.

System Shock 2
Everyone probably already knows about this game. If you haven't played this game then get it. This is one of those games that absolutely positively must be played.
Zork Grand Inquisitor is about the only game that I can call ''zany'', ''goofy'' and ''whimsical'' in a good way, without being sarcastic. It's the only Zork game I played, but I wish it wasn't the last in the series.

Best forgotten game ever, I swear! Here on GOG! Buy it!
Ghorpm: Maybe try to write a few words what make it so special, that would certainly be very helpful :)
3d puzzle/platformer with some shooting/action - much like Tomb Raider early games in general design.

However, in atmosphere and in delivery, much superior! The world of Shadowman is the dual-world of Voodoo. You are dealing with a back-and-forth between two worlds. The voice acting is marvelous. The level design is fantastic. The atmosphere is completely unique.

Bonus: there is a boss fight in a Vietnam War level which features the best Doors-imitation music ever created!

The game is fun enough to finish and then go back to play through again to try to and 100% find every item and collectible. A thing which I nev er do!