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.

H.E.R.O.

Atari 2600

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.

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

Galaga

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!

Freelancer, PC

Thief (1998)

Suikoden

Dance Dance Revolution.

(Do you feel old now?)

Sonic the Hedgehog 2 - Mega Drive

Final Fantasy Tactics

Bubble Bobble, Arcade, 1986

Metal Great Solid