Second post: All boxed and apparently complete:
CD-ROM:
The Simpsons Virtual Springfield
Discovery Channel Multimedia - Evolution
Star Control 3 (The box is *REALLY* ratty and falling apart, though.)
Sam and Max Hit the Road (Lucasarts, doesn't have a box, just a still-sealed bag containing a small jewel-case-sized cardboard case, plus a larger manual in the bag with it. Second manual included outside the bag.)
Games from small publishers, 5.25" disks in small boxes:
Buzzard Bait - Sirius Software
Space Strike - Datamost, Inc
Galactic Gladiators - RapidFire Games (apparently a division of SSI)
Epidemic! - RapidFire Games
The Warp Factor - RapidFire Games (a *VERY* obvious Star Trek ripoff, the ships on the cover are very obviously Star Trek designs)
Rack 'em up - Roklan Software (Billiards/Pool)
Maxis:
SimEarth for Windows (plus a bonus SimEarth for Macintosh manual) 3.5" disks
ROME Pathway to Power - 3.5" & 5.25" disks
SimCity Graphics Alternate Architecture Set 2: Future U.S.A., Future Europe, Moon Colony - 5.25" disks
Telarium Games, in "folio" style packages, both based on books:
Dragonworld
Fahrenheit 451
Avalon Hill "Microcomputer Games" (in large but thin boxes, containing A4 sized instruction sheets):
Galaxy
Andromeda Conquest
Lucasfilm Games:
Zak McKracken
Monkey Island
Other, standard size boxes:
Tongue of the Fatman - Activision
Star Control - Accolade
Merchant Prince - OOP
Robot Rascals - EA
Sargon III - Hayden Software "The Ultimate in Computer Chess"
A couple of big names, both apparently from their original releases:
Wizardry
Lemmings
Ulysses and the Golden Fleece - Sierra On-Line Inc. Yup, one of their earliest. This doesn't have a box, but appears to have all original contents. I think it was a "shrink-wrapped everything inside the manual" type.
Microsoft Adventure. In IBM branding, in an IBM plastic folio.
Microsoft Flight Simulator 1.0 - complete in box. This is the main reason I got this set of games.
Ultima IV Quest of the Avatar - Origin Systems
Worlds of Ultima - The Savage Empire
Worlds of Ultima 2 - Martian Dreams
Sid Meyer's Civilization
The Bard's Tale - EA
And, the piece de resistance, the Infocom sets:
Folios:
Deadline
Infidel
Sorcerer
Gray boxes:
A Mind Forever Voyaging
Suspended
And, last, but certainly not least: The Hitchhiker's Guide to the Galaxy