I've been raiding my local Value Village for old PC CD-ROM games. It's a gold mine at times! And the discs are almost always in perfect condition, too. They don't sell with boxes anymore sadly (except small boxes sometimes), but jewel cases a plenty. I've gotten the following games from there:
Loom CD
X-Wing Collector's CD
Mech Warrior 2
Mech Warrior 2 Expansion
Broken Sword 2
No One Lives Forever GOTY
No One Lives Forever 2
Prince of Persia Sands of Time
Driver
C&C Tiberian Sun
Rogue Squadron 3D
AVP2
Journeyman Project 2: Buried in Time
Knights of the Old Republic
Serious Sam TFE
Serious Sam TSE
The Dig
Warcraft II (Battle.net)
Unreal Tournament
Unreal (not gold)
Rebel Assault II
Torin's Passage
Quest for Glory Anthology
Shivers
Lost Mind of Dr Brain
Return to Krondor
Kyrandia 1
Morrowind GOTY
Wing Commander 3
Wing Commander 4
Lemmings CD
Half-Life GOTY
Blue Shift
Before they stopped selling big boxes I found brand new copies of Duke Nukem 3D Atomic, DukeZone!, and Duke Xtreme brand new. Never opened (except by Value Village to check the contents, I guess). I also found the X-Files game and Homeworld GOTY.
X-Wing Collector's CD came with the manual for X-Wing vs Tie Fighter but not the game 🙁. Also found the first C&C but it only had disc 2 included. So you can bum out sometimes, but usually it's pretty good. Thrift stores can be a gold mine