Some of these I have listed on eBay, most I don't. Make me some offers. All are in big boxes (of course).
Blood special edition (sealed, 2 copies available)
Daikatana (sealed)
Dark Forces (opened box, sealed jewel case inside)
Darklands (disks still sealed)
Descent II (sealed)
Doom Collector's Edition
Doom II for Windows 95 (sealed, box is kind of rough)
Doom II master levels (sealed)
Doom III promo box
Duke Nukem 3D: Atomic Edition (holographic box variant)
Fallout
Fallout 2
Gunship 2000 Philippine Islands and Antarctica scenario pack
Heretic
Hexen
Klingon Honor Guard (sealed)
Lode Runner: The Legend Returns
Mortal Kombat (2 available, both include tattoos, one is missing the manual)
Quake 2: The Reckoning
Resident Evil
Resident Evil 2 Platinum
Resident Evil 3
Return to Castle Wolfenstein
Return to Castle Wolfenstein collector's tin (3 available)
Rise of the Triad: Dark War
Shadow Warrior: Unlock the Secrets (sealed)
Sierra Fun Pack (from 1992, comes on about 10 floppies)
Spear of Destiny
Spear of Destiny Super CD Pack
Star Trek: Armada
Star Wars: Rebel Assault
Strike Commander
The Temple of Elemental Evil
The Ultimate Doom (3.5 floppy version, includes poster)
The Wheel of Time
Total War for WarCraft II
WarCraft II: Beyond the Dark Portal
WarCraft II: Tides of Darkness
WarCraft (MS-DOS release)
Wing Commander (incl ship blueprints)
Witchaven Interactive Preview
Wolfenstein 3d
Wolfenstein 3d shareware/Doom shareware 2-pack (sealed, 2 available)
W! Zone for WarCraft II (sealed)
X-Men: The Ravages of Apocalypse (tear in the back where it was opened, includes comic book)