Cyberstorm 1 & 2.

Most anything else I can think of from the 90s is dinky Shareware progrums.

Tass Times in Tone Town

Warhammer: Dark Omen
Space Crusade
Space Hulk 2: Vengance of the Blood Angels
Fade to Black
Cinemaware collection (you can get it on Steam)

I was just going to say Dungeon Master. It's only recently I've gotten into RPGs, after mostly playing Simulation/Point&Click Adventure/Platformer games. Even then I've mostly been playing isometric turn-based ones, such as the ones from Spiderweb. But I downloaded Dungeon Master from one of the abandonware sites and I love it. I love the graphics, and amazingly, most of all, I love mapping out the areas on graph paper. Seriously, when I get round to playing Legend of Grimrock, I'm turning off the auto-map! I basically bought every dungeon crawler on GOG that doesn't have automapping as a result.

Other than Dungeon Master, I'd quite like some more old Maxis games, in particular, SimFarm, and the VGA version of Space Quest 1 would be nice. I also wouldn't mind seeing some Simpsons games on here. I still have a CD copy of Virtual Springfield that works on my Windows 7 laptop.

American Mcgee's Alice

Heart of Darkness

In addition to the ones already mentioned, I think Rise of Nations is one of the most accomplished classic strategy games. The RTS that feels the most like building an everlasting empire.

I would also like to mention a lesser-known point-and-click adventure, The Lost Files Of Sherlock Holmes: The Case Of The Serrated Scalpel. Well-written, terrific atmosphere, good (and hard!) puzzles, art style that holds up to this day.

Hunter Hunted (platform game)
Croc 1 & 2 (3d platform games)
Adventures of Micro Man (platform game)
Super Street Fighter II Turbo (DOS version)
Missionforce: Cyberstorm (TBS), (sequel (Cyberstorm 2: Corporate Wars) is not bad either
Heretic 2 (third-person action game)
Captain Claw (platform game)
Gruntz (mix of RTS and puzzle game)
Get Medieval (nice clone of Gauntlet)
Kingdom Under Fire (Gold Edition) - RTS from 2001 (technically it's not 90' anymore, but "close")
Outlive (RTS)

The Reap
Firepower
Returnfire 1+2
Desert Strike
Jungle Strike
Nuclear Strike
Futurecop LAPD
D\Generation
Star Crusader
Starlancer
Freelancer
Mass Destruction
Hardwar
Motorhead
GTA 1+2
One Must Fall 2097
Solar Winds 1+2

Discworld Noir
No One Lives Forever
Blade Runner

Ecstatica 1+2
F-29 Retaliator
TFX
EF2000
Epic
Inferno
Lander
Assault Rigs
Heretic 1+2
Hexen 1+2
Take No Prisoners
Lemmings
Stunts
C&C + Red Alert
Warcraft 1+2
Starcraft
Blackthorne
The Lost Vikings
Darker
Pyrotechnica
Adventure Pinball 3D
Harrier Assault
Comanche: Maximum Overkill

Lemmings
Warcraft 2
Lemmings
No One Lives Forever
Lemmings
Stunts - 4D Sports Driving
Lemmings
Ms. Pac Man
Lemmings
Paradroid
Lemmings