Looking at that list I see I missed more games:
Carmen Sandiego (a classic)
Zool
Indiana Jones and the Last Crusade
Duke Nukem
Oh No More Lemmings
Aladdin
The Lion King
Commander Keen Episode 4: Secret of The Oracle (fantastic game)
4D Boxing (another classic)

Man, you made me remember 4d Boxing, even now, more than ten years after I played it, I can remember the a lot of the names of the fighters (Larry Lunchbucket, anyone?)

Dune II was awesome. It was my first RTS.

The lack of Betrayal at Krondor in this thread makes me sad...It's free to download now, so if you haven't yet now's the time, folks!

Dune II was every person's first RTS.
Everyone got here before me so I really can't add additional names, but Dune I was also pretty fun, if you had any idea of what you were doing. We also stayed with DOS for a bit longer so I guess I can add these:
DOOM
Duke Nukem 3D
Blackthrone
The Lost Vikings
Warcraft: Orcs and Humans

Windows gaming didn't really take off until DirectX (1996/7) was released it was simply easier to directly access the video chip and memory from Dos then go through windows.

Lemmings
Knights of the Sky
Reunion
Nova Storm
Zool 2
Lotus 3
Worms
Starfighter
MegaRace

And more demo games then I can count :)

one game only... Daggerfall

way too many games to list. Some that haven't been listed though

Syndicate
Quest for Glory 1 & 2
Space Quest series
Wing Commander 1 & 2
Stunts
Budokan
Populous
Centurion: Defender of Rome
SSI: Gold Box series
Civilization 1(my favorite version)
Eye of the Beholder
Ultima
X-Com(deserved to be mentioned more than once)
...
so many more

The only games I can remember playing were Sim City 2000, X-Wing, and Tie Fighter.

My favorite games & companies from the DOS era:

LucasArts:
The Secret of Monkey Island, Monkey Island 2: LeChuck's Revenge, Indiana Jones and the Fate of Atlantis, Full Throttle, Maniac Mansion: Day of the Tentacle, Sam & Max Hit the Road, X-Wing, Rebel Assault (the game that moved CD-Rom drives in 1993; took me several days to get it running)

Westwood:
Dune II, Command & Conquer, The Legend of Kyrandia, The Legend of Kyrandia: Hand of Fate, The Legend of Kyrandia: Malcolm's Revenge, Lands of Lore: The Throne of Chaos

Bullfrog:
Dungeon Keeper, Magic Carpet, Syndicate, Populous, Theme Park

Origin:
Strike Commander, Ultima VIII: Pagan, Wing Commander III: Heart of the Tiger, Wing Commander: Privateer, BioForge

Looking Glass:
System Shock, Car & Driver (the predecessor of the Need For Speed series)

Microprose:
Civilization, Colonization, Grand Prix (aka World Circuit), Grand Prix 2, Master of Orion, Master of Magic, Pirates! Gold, Railroad Tycoon, Transport Tycoon

Interplay:
Descent, Fallout, Star Trek: Judgment Rites, Star Trek: 25th Anniversary, Stonekeep

Blizzard:
Warcraft: Orcs & Humans, Warcraft II, The Lost Vikings

Other favorites:
Betrayal at Krondor (Dynamix)
SimCity 2000 (Maxis)
Simon the Sorcerer 1 & 2 (Adventuresoft)
Broken Sword 1, Beneath a Steel Sky (Revolution Software)
Comanche: Maximum Overkill (Novalogic)
The Settlers, The Settlers II, Battle Isle 2, Schleichfahrt (BlueByte)
Commander Keen: Goodbye Galaxy (id/Apogee)
Jagged Alliance (Sir-tech)
Star Trek: The Next Generation - A Final Unity (Spectrum Holobyte)
Outcast (Infogrames)
Anstoss, The Patrician, Elizabeth I., Hanse: The Expedition (Ascaron)
Summer Challenge, Winter Challenge (Accolade)

Other legendary DOS games:
Doom, Hexen, Duke Nukem 3D, Ultima Underworld: The Stygian Abyss, Ultima Underworld II: Labyrinth of Worlds, Ultima I-VII, Wing Commander I & II, Silent Service I & II, X-COM series, Red Baron, 1942: The Pacific Air War, F-15 Strike Eagle II, Falcon series, Alone in the Dark, The Bard's Tale Trilogy, Eye of the Beholder Trilogy, MDK, Aces of the Deep, Aces over Pacific, King's Quest series, Quest For Glory series, Leisure Suit Larry series, Space Quest series, Police Quest series, Gabriel Knight series, Gobliins series, Wizardry series, Heroes of Might & Magic series, Might & Magic series, Chuck Yeager's Air Combat, Jane's Combat Simulations: AH-64D Longbow, LHX: Attack Chopper, Wasteland, Link 386 Pro

5¼ and 3½-inch goodness. DOS was my NES. The introduction to video gaming.

After 1990 I used Windows 3, but well that's just a shell anyway. Back then I loved all the sierra adventure games.