Wow, too many to list. Looking through my shelves i'd say:
Grim Fandango
Wing Commander 1-5
Privateer 1 & 2
Strike Commander
Bioshock
System Shock 1 & 2
Ultima 7-9
Ultima Underworld 1 & 2
MDK 1 & 2
Max Payne 1 & 2
Unreal 1 & 2
Phantasmagoria 1 & 2
Kings Quest 1 - 7
Space Quest 1 - 6
Leisure Suit Larry 1 - 7
Police Quest 1 - 4
Maniac Mansion
Day of the Tentacle
The Dig
Broken Sword 1 - 4
Colonization
Civilization 1 - 4
Warcraft 1 - 3
Starcraft
Grand Theft Auto 1 - 3, Vice City, San Andreas
Outlaws
Indiana Jones and the Fate of Atlantis
Indiana Jones and the last Crusade
Gothic 1 - 3
Doom 1 -3
Hexen 1 & 2
Quake 1 - 4
Deus EX 1 & 2
Might & Magic 1 - 7
Gobliins, Gobliins & Goblins
Heart of China
Rise of the Dragon
Red Baron
Comanche 1 - 3
Mad TV
Battle Isle 1 - 4
History Lines 1914 - 1918
The Legend of Kyrandia 1 - 3
Lands of Lore 1 - 3
Freddy Pharkas
Runaway 1 & 2
Willy Beamish
Gabriel Knight 1 - 3
Shadowcaster
Crusader: No Remorse
Crusader: No Regret
Heretic 1 & 2
Wizardry 1 - 7
Winter Games
Summer Games
Kingpin: Life of Crime
Tomb Raider 1 - 6
Quest for Glory 1 - 5
Alien vs. Predator 1 & 2
X-Wing
Tie-Fighter
Star Wars: Dark Forces
Star Wars: Jedi Knight 1 & 2
Star Wars: Knights of the old Republic 1 & 2
Fallout 1 & 2
Magic Carpet 1 & 2
Theme Hospital
Theme Park 1 & 2
The incredible Machine etc.
Lemmings 1 - 3
Worms 1 & 2
Formula One Grand Prix 1 - 4
Alone in the Dark 1 - 4
Wolfenstein 3D
Return to Castle Wolfenstein
Commander Keen 1 - 6
Prince of Persia 1 & 2
Out of this World aka Another World
Flashback
Grim Fandango
Wing Commander 1-5
Privateer 1 & 2
Strike Commander
Bioshock
System Shock 1 & 2
Ultima 7-9
Ultima Underworld 1 & 2
MDK 1 & 2
Max Payne 1 & 2
Unreal 1 & 2
Phantasmagoria 1 & 2
Kings Quest 1 - 7
Space Quest 1 - 6
Leisure Suit Larry 1 - 7
Police Quest 1 - 4
Maniac Mansion
Day of the Tentacle
The Dig
Broken Sword 1 - 4
Colonization
Civilization 1 - 4
Warcraft 1 - 3
Starcraft
Grand Theft Auto 1 - 3, Vice City, San Andreas
Outlaws
Indiana Jones and the Fate of Atlantis
Indiana Jones and the last Crusade
Gothic 1 - 3
Doom 1 -3
Hexen 1 & 2
Quake 1 - 4
Deus EX 1 & 2
Might & Magic 1 - 7
Gobliins, Gobliins & Goblins
Heart of China
Rise of the Dragon
Red Baron
Comanche 1 - 3
Mad TV
Battle Isle 1 - 4
History Lines 1914 - 1918
The Legend of Kyrandia 1 - 3
Lands of Lore 1 - 3
Freddy Pharkas
Runaway 1 & 2
Willy Beamish
Gabriel Knight 1 - 3
Shadowcaster
Crusader: No Remorse
Crusader: No Regret
Heretic 1 & 2
Wizardry 1 - 7
Winter Games
Summer Games
Kingpin: Life of Crime
Tomb Raider 1 - 6
Quest for Glory 1 - 5
Alien vs. Predator 1 & 2
X-Wing
Tie-Fighter
Star Wars: Dark Forces
Star Wars: Jedi Knight 1 & 2
Star Wars: Knights of the old Republic 1 & 2
Fallout 1 & 2
Magic Carpet 1 & 2
Theme Hospital
Theme Park 1 & 2
The incredible Machine etc.
Lemmings 1 - 3
Worms 1 & 2
Formula One Grand Prix 1 - 4
Alone in the Dark 1 - 4
Wolfenstein 3D
Return to Castle Wolfenstein
Commander Keen 1 - 6
Prince of Persia 1 & 2
Out of this World aka Another World
Flashback