Listed in order of (re)release.

Pizza Tycoon
Pizza Tycoon 2
Sea Dogs: City of Abandoned Ships
Ignition
Tachyon: The Fringe
Ceville (re-added to the catalogue after having been removed)
Lost Eden
Imperium Galactica II: Alliances (apparently a PC version of a mobile port of the original game)
SWAT 4: Gold Edition
Constructor (since renamed Constructor Classic 1997) (re-added to the catalogue after having been removed)
Freddy Pharkas: Frontier Pharmacist
Emperor: Rise of the Middle Kingdom
Caesar
Caesar II
Dear Esther: Landmark Edition (remaster) (borderline case, as the original mod was from ca. 2008, while the first standalone commercial version released in 2012)
The Colonel's Bequest
The Dagger of Amon Ra
Hidden & Dangerous Action Pack
Hidden & Dangerous 2: Courage Under Fire
The Adventures of Willy Beamish
Turok 2: Seeds of Evil (remaster)
Army Men RTS
Delta Force
Delta Force 2
Delta Force: Land Warrior
Delta Force: Task Force Dagger
Delta Force: Black Hawk Down Platinum Pack
Delta Force Xtreme
Pray for Death
Planescape: Torment: Enhanced Edition (remaster) (borderline case, as it replaced [but still includes a separate copy of] the "classic" Planescape: Torment)
Codename: ICEMAN
SpellForce 2 - Anniversary Edition (remaster) (borderline case, as it replaced the games whose content it contains [Spellforce 2: Shadow Wars & Spellforce 2: Dragon Storm])
Full Throttle Remastered (remaster)
de Blob (remastered port)
Legends of Heroes: Trails in the Sky the 3rd (port) (borderline case, as the original Japanese PC version released in 2007)
Conquests of Camelot: The Search for the Grail
Conquests of the Longbow: The Legend of Robin Hood
Empires: Dawn of the Modern World
Throne of Darkness
Metal Slug
Metal Slug 2
Metal Slug 3
Metal Slug X
Fatal Fury Special
Samurai Shodown 2
Samurai Shodown V Special
The King of Fighters 2000
The King of Fighters 2002
The Last Blade
Blazing Star
Baseball Stars 2
Shock Troopers
Twinkle Star Sprites
King of the Monsters
Lock's Quest (remastered port)
The Elder Scrolls IV: Oblivion Game of the Year Edition Deluxe
Fallout 3: Game of the Year Edition
Wonder Boy: The Dragon's Trap (probably closer to a full-on remake than to a remaster, but it CAN be played with the original's graphics & sound, so I included it)
Homeworld: Emergence (f.k.a. Homeworld: Cataclysm)
Tender Loving Care (apparently a PC version of a recent mobile port of the game)
Mob Rule Classic (re-added to the catalogue after having been removed [as Mob Rule])
The Humans Bundle
Sudden Strike Gold
Sudden Strike 2 Gold
Sudden Strike 3
Alien Rampage
Quake 4
Doom 3: BFG Edition (revised re-release) (borderline case, as the original game was from 2004, while this version was released for PC in 2012)
Ys SEVEN (port) (the original handheld version first released in 2009)
The Suffering
The Suffering: Ties that Bind
Sengoku 3
Real Bout Fatal Fury 2: The Newcomers
Pulstar
Art of Fighting 2
Neo Turf Masters
Shock Troopers: 2nd Squad
Garou: Mark of the Wolves
Ironclad
Rogue Trooper Redux (remaster of a game from 2006 [which was already -- and is still -- sold separately on GOG in its original form])
Mafia
A.D. 2044
Reah: Face the Unknown
Schizm: Mysterious Journey
Crime Cities
Robo Rumble
Call of Cthulhu: Dark Corners of the Earth [since removed]
Conqueror A.D. 1086
Heart of China
Rise of the Dragon
NecroVisioN
Sphinx and the Cursed Mummy (port of a console game from 2003)
Helldorado
Descent (re-added to the catalogue after having been removed)
Descent 2 (re-added to the catalogue after having been removed)
Descent 3 + Mercenary (re-added to the catalogue after having been removed)
Jazz Jackrabbit Collection
Jazz Jackrabbit 2 Collection
Epic Pinball: The Complete Collection
Star Wars - The Force Unleashed Ultimate Sith Edition
LEGO Star Wars: The Complete Saga
Titanic: Adventure Out of Time