Only a few:

Nox
Myst
Baldur's Gate 4 in 1 set

Not a lot of them, I think this is all.

Baldur's Gate
Baldur's Gate II w/ Throne of Bhal
Icewind Dale
Icewind Dale II
Neverwinter Nights Diamond
Fallout
Fallout 2
Fallout Tactics
Age of Wonders
Age of Wonders II
Gothic 3
Two Worlds
The Witcher: Enhanced Edition
The Witcher 2
Far Cry
Temple of Elemental Evil
Empire Earth


The AD&D games are all the old big boxes, the others are the more modern, small boxes. I do miss games coming in boxes the size of a couch cushion. Those were good times.

Descent: Freespace
FarCry
Freespace 2
Iron Storm (it sucks, the box art is good)
Painkiller: Black Edition
Prince of Persia: Sands of Time
Riven: Sequel to Myst
Serious Sam: Second Encounter
Tom Clancy's Ghost Recon
Tom Clancy's Rainbow Six Gold
Unreal (big box)
Unreal Tournament GOTY
Unreal Tournament 2004

Baldurs Gate Tales of the sword Coast, Shadows of Amn, and Throne of Bahll
Icewind Dale 1 and 2
Temple of elemental evil
Neverwinter Nights Diamond addition
Divine Divinity
Fallout 1, 2 and Tactics
The witcher Enhanced addition
Freespace and expansion
Blood Rayne
Oddworld Abe's Oddysee
Stronghold, Stronghold Crusasder
All the Unreals

Baldur's Gate 2
Icewind Dale
Neverwinter Nights

Wow.. pretty good list you have there OP. Here is mine:

Another World (original floppy)
Aquanox
Aquanox 2
Arcanum
Baldurs Gate
Baldurs Gate 2
Battle Chest
Beyond Divinity
Descent
Descent 2
Descent 3
Divine Divinity
Dungeon Keeper
Earthworm Jim
Empire Earth
Fallout
Fallout 2
Freespace
Freespace 2
Giants
Gothic
Gothic 2
Gothic 3
Hagemonia
IWD
IWD 2
The Incredible Machine
Iwar
Iwar2
Kings Quest 4+5+6
Kings Quest 7
Lionheart
The longest Journey
Master of Magic
Master of Orion 2
Myst
NWN
PST
Riven
Sacred Gold
Stoonekeep
TOEE
Ultima 7
Unreal
Unreal Tournament
Unreal 2
Unreal 2004
Vampire TMR
Wing Commander Privateer
Wing Commander 1+2
Wing Commander 3
Witcher Enhanced

Yes... So sad is my life. lol... Most of the games that I have picked up on GOG I have given the boxed copies away to friends... (Even my BG2 Collectors Box with Gold color Cd's) :-) Sad how married life and children have changed my priorities when it comes to collecting things... Although I get to cheat with these digital copies.. Clears up space and I still get to keep my game and all the goodies... haha :-)

Absolutely certain I have disc copies of SimCity 2K and Alpha Centauri around *somewhere*...