It was not there for a long time.

List got a clean up. I do not know how to link to that huge explanation of ARMA vs OFP, so I left it alone until someone can explain to me how to do that.

Deponia 2: Chaos on Deponia is missing the manual.

MOO3 missing reference card.

A minor feelie, but Deus Ex is missing the evidence posterboard (back of the newspaper). This might be a regional difference...my version also has a slightly different newspaper.

I think that music problem is solved, as it is said so by bengeddes here.

Main problem, now, with DD is listed by bengeddes and explained by Raze_Larian [url=http://www.gog.com/forum/divine_divinity_series/what_are_the_problems_with_gogs_divine_divinity/post102]here,
but maybe when Larian has time, after releasing Original Sin, they will fix DD, hopefully.

Bi-monthly update ;-P

Dungeon Keeper 2 - Still the problem with the pre-patched version 1.7 which features a broken AI in contrast to previous versions 1.51 or 1.3. (link)
A simple solution for GOG, add as alternative download the vanilla version 1.3 (+patches) under extras.

Also, the v1.7 recruitment bug fix is not included in the official packages nor is this fix at least stickied in the forum tree, newbies will not find the fix.

Chaos Overlords has some sound issues - see forum thread here:
-The soundtrack does not start playing until you select a track from the menu.
-The music does not shuffle properly in-game; instead, the same track loops over and over. This is disappointing as the game has an excellent soundtrack. User LanceCrossfire has come up with a sort-of fix here.
-Some users report a "system alert" beep playing after every combat round. See here.

In GOG's defense, I would note that Chaos Overlords has always had sound issues running on modern systems, and the GOG version works better than any other I'm aware of (most won't play any music at all). I just hope they can get the last few bugs ironed out.

Total Annihilation's map_editor.exe not compatible with Windows 8.1 preview, or just Windows 8

I don't know if this qualifies as broken, but Kingpin: Life of crime is one wobbly affair.
The game is playable, but all the characters wobble which makes them right out disgusting to look at (more that they originally were intended to be).

I'm playing on Windows 7 Ultimate 64 bit with an ATI Mobility Radeon 5470 gfx.

Yeah, it was like that since day one. Nothing to do with GOG.

"Two Worlds" lip-sync fix: http://www.gog.com/forum/two_worlds_series/npcs_do_not_lip_sync

"Psychonauts" missing latest patch version. Fixed by vooodooman http://www.gog.com/forum/psychonauts/psychonauts_patch_1_05_retail_gog_and_other_dd_officially_unofficial_release/page1

Both should be added to "fixed by community" section in this thread and stickied or included by GOG in the game installers.

I just tried Divine Divinity, and music is still broken in GOG version. Manual fix is posted by Raze here:
http://www.gog.com/forum/divine_divinity_series/dd_is_the_music_still_broken/post4
Maybe GOG is waiting for bigger patch from Larian...

Add this problem to the list:
Carmageddon 2:
Cannot start the game. CARMA2_HW.exe crashes upon startup. Contacted tech support, they said unplug your 360 USB controller. Did so, even unplugged my external USB harddrive just in case. Cannot disconnect USB keyboard and mouse, for obvious reasons. Still crashes.

More info here: http://www.gog.com/forum/carmageddon_series/carma2_hwexe_has_stopped_working

Mobile Forces was removed from the catalogue some time ago.