Might & Magic VII (PC)

Oddworld: Abe's Oddysee (PS1)

So many games that I even upvoted that are still absolutely amazing haven't really aged perfectly control- or gameplay-wise, but Oddworld could be released today and it would still be perfect.

I missed System Shock 1 and 2 on release (I was 1 and 6 years old, respectively) but I've recently been playing the SS1 remake and, holy shit, this is an incredible game.

I think the original is held back by its UI but the actual game itself, which the remake pretty much preserves almost one to one, is incredibly solid even by modern standards. I've been super hooked on it and it's opened my eyes to an entire lineage of games that I've not paid attention to - System Shock 2, Deus Ex, and Prey are the big three that I have my eye on when I finish with SS1 Remake.

Xenogears

Metal Slug

Day of the Tentacle - PC

It just barely makes the cut off since it came out in 99, but Sid Meier's Alpha Centauri is my favorite strategy game of all time. It even managed to get a Linux port and you can get it on GOG. I was excited when Civ: Beyond Earth was announced that it would be a true successor, but sadly it wasn't even close.

Castlevania: Symphony of the Night

Edit: nevermind, this was already posted. I literally did a search on the page first and it didn't match for some reason.

Galaga

H.E.R.O.

Atari 2600

Legacy of the Wizard - NES aka Dragon Slayer IV Drasle Family - MSX

Zork

Perfect Dark, N64

I am very sad that I've scrolled several pages and haven't seen the obvious one (though I could just be blind):

Deus Ex.

Edit: or perhaps it's because Deus Ex is from 2000 and I don't know if it counts yet. Maybe I'll wait 'til next year!

Thief (1998)

Freelancer, PC

Suikoden

Dance Dance Revolution.

(Do you feel old now?)

Sonic the Hedgehog 2 - Mega Drive