In no particular order as I find them:
Icewind Dale II (3 discs w/bonus)
Icewind Dale (With Heart of Winter, soundtrack and bonus, 5 discs)
Baldur's Gate (collection w/Tales of the Sword Coast, 6 discs)
Frank Herbert's Dune (the 2001 one, crappy adventure game)
Septerra Core
Morrowind (collection with Tribunal, Bloodmoon and construction set, 4 discs)
Final Fantasy 7 (4 discs)
Zork Anthology +Nemesis (4 discs)
Fallout
Fallout 2
Fallout Tactics (3 discs)
Dark Forces 3: Jedi Knight 2: Jedi Outcast (I love titling it like that... 2 discs)
X-Wing: Alliance (2 discs)
Dark Forces 2: Jedi Knight (2 discs)
Star Wars: Force Commander (2 discs... what?! Don't look at me like that! I picked it up for fifty cents!)
Age of Mythology: Gold Edition (2 discs)
Rise of Nations (w/Thrones & Patriots expansion, 2 discs)
Dungeon Keeper
Dungeon Keeper 2
Pax Imperia
Battle Realms
Dark Planet: Battle for Natrolis (there was a time when I picked up every 4th-rate RTS I found for under $5)
Warcraft II: Battle.net edition
C&C Generals (with Zero Hour Expansion, 4 discs)
Total Annihilation (2 discs)
Starcraft (w/Brood War, 2 discs)
Descent: Freespace (w/Silent Threat, 3 discs)
Freespace 2 (3 discs)
Descent 3 (w/Mercenary, 3 discs)
Freelancer
Need For Speed: Underground (2 discs)
Quake III: Arena
Return to Castle Wolfenstein
Unreal Tournament (first release, 2 discs)
Unreal 2 (2 discs)
Unreal Tournament 2004 (6 discs)
Unreal Tournament Game of the Year edition (it came bundled with 2004, 2 discs)
XIII (4 discs)
Giants: Citizen Kabuto (2 discs)
Aliens vs Predator (2 discs)
C&C: Renegade (2 discs)
Rainbow Six (the first one)
Sin
No One Lives Forever (2 discs)
the Chronicles of Riddick: Escape from Butcher Bay (5 discs)
Freedom Fighters
Rune (w/Halls of Valhalla, 2 discs)
City of Heroes (RIP, 2 discs)
Populous: the Beginning
Sacrifice
Messiah (2 discs)
Dark Side of the Moon (adventure game, 6 discs)
Aqua Nox
Sim City 2000
Sim Earth
Simpson's Hit and Run (3 discs)
Evil Dead: Hail to the King (2 discs)
Blackthorne (that's right, DOS, 1994, Interplay/Blizzard, on CD)
Crusader: No Remorse
Crusader: No Regret
Syndicate Wars
Mechwarrior 4 (Vengeance, Mercenaries and Black Knight, 5 discs)
Torchlight (worst hardcopy of anything ever... glad I got a Steam copy with TL2)
Alice (2 discs)
Warlords Battlecry III
Warlords IV: Heroes of Etheria
Armed and Dangerous (2 discs)
Vampire the Masquerade: Bloodlines (3 discs)
Driver
Fallout 3 (still in the lunchbox, also with Point Lookout and Broken Steel on a disc, so 2 discs)
Sins of a Solar Empire: Trinity
C&C: The First Decade (w/bonus DVD, 2 discs)
Galactic Civilizations II Gold Edition (Dread Lords and Dark Avatar, 2 discs)
Supreme Commander
Supreme Commander: Forged Alliance
Portal (no, not in the Orange Box. I bought it separate on purpose... it's also the reason I have a Steam account)
Mass Effect (...I appear to be missing a disc... only found disc 1)
Mass Effect 2 (2 discs)
Deus Ex: Invisible War (2 discs)
Dragon Age: Origins
Knights of the Old Republic (4 discs)
Starcraft 2: Wings of Liberty
Fallout: New Vegas
X3: Reunion (6 discs)
Lord of the Rings: Battle for Middle Earth Anthology (I, II, bonus DVD for II, game manuals, 4 discs)
Company of Heroes: Game of the Year edition
Unreal Anthology (2 discs)
Assassin's Creed (the worst port I've ever had the misfortune of owning... no desire to try playing it again)
Dawn of War 2 (with Chaos Rising, 2 discs)
Arcanum
Neverwinter Nights: Diamond edition
Oblivion (in the NWN box, I think my brother lost the packaging...)
Star Wars: the Old Republic (3 discs)
Fallen Earth: Blood Sports
Frontlines: Fuel of War (2 discs)
M.A.X. Mechanized Assault and Exploration
Others I know I have that I'm not crawling into my attic to find:
Driver 3
Evil Genius
Dune 2000
Homeworld and HW2
Diablo and Diablo 2 with expansions
AvP2
Dawn of War (with Dark Crusade and Soulstorm)
Borderlands
Mechwarrior 2
Mechwarrior 3 with expansions
Quake 4
Spore
Star Wars: Galactic Battlegrounds with expansions... I think it was just called "Saga".
Dark Forces
Dark Forces 4: Jedi Knight 3: Jedi Academy (I still love all those silly titles)
City of Villains collector's edition
Motor City Online
Half Life (with.... expansions. Hard to remember)
Deus Ex. Surprised that one's MIA.
Thief 2: the Metal Age
Warcraft
Warcraft 3
Vampire the Masquerade: Redemption
X-Wing (on 3.5" floppy)
TIE Fighter (on 3.5" floppy)
X-Wing vs TIE Fighter
...I'm sure there are a whole lot more in there that I've forgotten...