X-COM: UFO Defense
There was some action game from a top down perspective where a guy in red with a helmet like a Roman centurion was a vicious executor for the State in the future. He rebels. Can't recall the name. It was innovative for the control scheme at the time, which let him roll to the side to dodge stuff or get into position. Super fun, great explosions, partially destructible and for its time very beautifully done environment. Awesome fighting and manning of robot sentries.
Magic Carpet -- Huge fun FPS that let you fly as you shot around. Much copied sound effects.
Comanche -- the first one

yeah, i got the cd version, the floppy version, and the download version from bethesda. but i would pay money for a version i didnt have to use dosbox with.

Omg, how could i forget dungeon keeper! Populous: the beginning would be awesome, had that on disc but i lost it years ago during a move.

It would be really nice to have Riven (and the rest of the Myst series) running from the harddrive, especially given Gametap's lack of 64bit support.
Thanks for this wonderful service!

I would also like to put my vote in for following games in no particular order
bolded ones i would really like
Independence War 1 & 2
Hardwar
Battlezone 1 & 2
Thief 1 & 2
Starflight & Protostar
Hardnova
System Shock 1 & 2
Baldur's Gate 1 & 2 + Expansion (with Widescreen&hires mods pre included in possible)
Planescape Torment
Heavy Gear 1 & 2
Omikron
Longest Journey
Anachronox
Outcast
Arx Fatalis
Moonbase Commander
X-Com
Battle Isle
Syndicate

All the DOS games on GOG are running in DOSBox, just with a premade config.

I concur with the calls for the Wizardry series! I took a party all the way from 6-8, and to be able to re-visit these classics on Vista would be awesome :D

Dungeon Keeper Gold edition most certainly is a must-have..!

Carmageddon series!

So much good taste here :) I'll just add my few recommendations to the pile. Most of these have probably been mentioned already, but I'm sure it won't hurt.
Mafia
Hidden & Dangerous 2 (and its expansion Sabre Squardon)
Incubation (and the Wilderness Missions expansion)
Dungeon Keeper 1 & 2
Anachronox
Outwars - great old jetpackin' troopers vs bugs combat game
Battlezone 1 & 2
HardWar
and loads more I've forgotten.
(EDIT: Like the No-One Lives Forever series, d'oh!)

Someone very noble (with a lot of time) should go through every page and tally up the most requested games so far. The top 10 or so. Then just remove all the other games.
The ones I've seen a lot of so far are Planescape Torment, Ultima series, Wing Commander series, Deus Ex, Crusader series.

Panzer Commander 2
Spy vs Spy
Worms
Airlines

Well if someone has the time for that, might has well do the full rank.

Sounds like a job for a person who runs this website? I'm not sure. Just seems like an awful lot of work, of continual work for just a member