In my opinion: Urban Chaos. It's like a GTA3 but a couple years earlier.
Third-person action-adventure with parkour elements, open city, driving(with awful physics) and some other stuff. That's was really good on PC for that time. But an era of third-person-lonely-shooters-saving-the-world will come a bit later.

CALL OF CTHULHU: DARK CORNERS OF THE EARTH!

How the hell did i forget that one? All those novelties in health system, environmental-screen signs replacing lifebar, insanity factor, shooting and targeting, were downright amazing! Had the game been bug-free, well-optimized and not rushed, it had the potential to set new benchmarks for the genre (horror, survival, shooter) and even make other shooters jealous enough to imitate gameplay elements found inside it (i particularly loved health/targeting systems and how they worked)!

I'm sure they've been mentioned already (and shame on you all if not), but:

Doom
Ultima Underworld
Ultima 7 (yes, the bread baking part)
Descent
Alone In The Dark

I'm just thinking is it nowadays near impossible to similarly make games ahead of their time? Back then people could come up with technological marvels and new ways, even new genres, but I am not really expecting nowadays anyone to make a new games whose graphics engine blows everything else away, something you feel you've never seen before (like at least I felt with the aforementioned games). Some indie games might come up with fresh new ideas once in awhile, but not technological breakthroughs.

It's definitely more difficult to make technological breakthrough today, as new technologies are either hard and costly to research, or they are too specific and not recognizable by majority of players. (Like there are a lot of devices for vehicle simulators that also have increased resolution for graphics, but most players just aren't interested in them)

But otherwise new ideas ahead of their time probably still pop up from time to time. Like Minecraft that was really changer for sandbox games.

I guess VR glasses, as now they finally seem to be usable (as they claim), is one modern gaming technology breakthrough. But I guess it can't be granted to one or few specific games, now many games are simply starting to take advantage of that new technology.

No I am not yet buying VR glasses, waiting for lower prices and standardization, and some analysis if it is a good idea to keep such LED screens close to eyes for several hours per day...

Minecraft s a good point, I guess it succeeded in something different. I liked it that the game author would sell the game for a long time only from his own store, staying fully independent in that regard. It is not a game for me though, I guess I want more challenge from my games generally.

Hentai3D / 3D SexVilla; sadly there is next to none publication I could find; much less one that concentrates on the technical aspects; character physics, visuals and interaction with objects and other characters (wipe the drool; we are being technical here :P ) which where faaaaaaaaaaaaaaaaaaaaaaaaaaaaaaar ahead of their time.

If you look at the models at the current versions it looks kind of cheapy (gone lazy by past success?) but (at least judging by screens) they have not changed much and back then that tech was mind blowing.

I do guess they are still dead boring after a few min :P

IIRC visually wise similar Japanese titles surpassed that quickly, but because of their censoring they never (last time I checked; long time ago) invested much if anything in interaction-animation & physics.

And tomorrow when I'm sober I probably regret I turned on the PC and visited the internet :P

No, no. That was Eddie Torres, the Extra Testicle. :P

Someone has an extra testicle?

Can I have it? I'm one short.

The Penumbra series, followed by Amnesia: The Dark Descent & SOMA (basically anything from Frictional Games).

I'm so used to seeing games where you just ran about killing things, but then I played these & from what I recall, I'd never seen any other games where you had to either hide or run for your life.

Nowadays, there's quite a few of them, but they were a rarity way back when :)

Fallout 1 can be beaten without violence IIRC,and a lot of early arcade games were about avoiding enemies, but I suppose you're right about it being rare on the whole.

Blackout was a dark and nasty adventure game from Denmark. The critics were positive, but ... unlike any other adventure games out there, this one had no puzzles whatsoever. So, asked the critics, could this truly be called a game? This was in 1997, a very long time before walking sims became a thing!

Never played any of the Fallout games.
Heard good things about (some) of them, but then I saw the whole "Aim, shoot, game pauses & you pick a body part to hit" & that noped the entire game for me hehe.

Hostile Waters: Anteaus Rising
Hostile Waters was way ahead of its time! It had a very cinematic feel in the cut-scenes and the gameplay was top-notch. It allowed the player to create futuristic tank-like vehicles from a carrier and then plot them out on the screen.

Kingpin
This was an FPS game that used the Quake 2 engine, but the gameplay mechanics were a lot more in depth. It had a mafia atmosphere and it played like an RPG with FPS elements.

Redline
This was an action game which allows the player to drive a car and walk around in FPS mode. It had a cyberpunk/post apocalyptic feel to it.

Rune
Rune was a real gem of a game! It's heavily based on Norse Mythology and had an epic quest for the player. This game is a must-play for all adventure fans!

Shogo MAD
Shogo MAD was a unique mech game with anime elements. The gameplay had an FPS mode and the player could also pilot a giant mech. This game unfortunately went head-to-head with Half-Life 1, and the rest is history.

Slave Zero
Another cyberpunk game with giant robots! What's not to like? :P