Original list: March 3, 2010. Last update: 05/07/2016.

Another thread about some of these same topics.

Removed all missing OST because work is being done in another thread. Broken sound / soundtracks will still be listed here.

This list is not exhaustive (and is not meant to be) or done all by myself. Many members on this thread and other forums have contributed to it. I am not going to individually credit each contribution, but I appreciate and thank everyone's help because this is a great online community.

More than likely, I'm forgetting things (much like our GOG overlords have done from time-to-time -- xP), so I apologize for this. I will try to keep this up-to-date. New stuff has '*' next to it. Nifty, isn't it? Let's go!

Games completely removed from the catalogue (Licensing unless noted)

ArmA - Whole series gone.
Chessmaster 9000 - Some hope.
Colin McRae Rally 2005 - No hope.
Cryostasis - Some hope.
Dark Matter - The reason is ending being not acceptable by players.
Mob Rule - Bought to be remastered.
Obscure - Some hope.
Operation Flashpoint - ArmA is the replacement, but it's missing Red Hammer expansion, which apparently sucked anyways.
Republic: The Revolution - Some hope.
Re-Volt - No comment.
Second Sight - Gone.
Space Rangers 1 & 2 - DEAD.
TOCA 3 - No hope.
Wallace & Gromit - Some hope.

Missing Items (soundtracks, reference cards, manuals, etc)

Age of Wonder Series - All missing manuals.
Baldur's Gate II - OST rip slightly off.
Book of Unwritten Tales - Missing Deluxe Edition.
Crusaders of Might and Magic - Missing manual.
Deponia 2: Chaos on Deponia - Missing manual.
Gabriel Knight 1 & 3 - Missing the graphic novel here. Credit to RakeeshSorrel.
Heroes Chronicles - Missing some manuals (specifics needed).
Jagged Alliance: Deadly Games - Missing manual.
Little Big Adventure 2 - Removed poster.
Might & Magic 8 - Missing map.
MOO3 - Reference card missing.
Patrician 1 - Map and handbook.
Pinball Gold Pack - All missing manuals.
Stonekeep - Missing the scans from the hardcover novel.
Waxworks - Manual is incomplete.
Zork Anthology - Apparently, we are missing a manual and a bunch of extras. Please check this thread for more information and places to download these.

DOS Vs. Windows or Floppy Vs. CD-ROM or Version variations ("inferior" titles, licensing issues, missing information, regional differences or content to be considered "complete")

Alone in the Dark 1-3 - Missing floppy version with original sound.
Battle Chess Special Edition - Apparently, GOG does not have the rights to the cinematics for this title. :-(
Capitalism games - We have no CD audio available; anywhere. For Capitalism II, I believe that the version on Enlight's site does have the full audio track.
Carmageddon II - Official Graphics Pack: It can be easily downloaded from the net and added to the GOG version, but it's value is debatable because the GOG version is probably superior.
Castles 1 + 2 - This is the CD-ROM version with various enhancements. Unfortunately, this version is missing many plots to make the game more interesting for players.
Dark Fall: The Journal - Missing original version with different audio in some rooms.
Earthworm Jim 1 + 2 - First game is not Special Edition with extra levels.
Fallout 1 + 2 - Censored versions (no killing kids, references to drugs removed, no nudity). Fix available via patches.
King's Quest - Missing King's Quest 1 SCI version and King's Quest 4 AGI version.
M.A.X. - DOS Version.
*Megabyte Punch - Special Edition available with extra levels.
Normality - Spindown: "Normality is the original UK version with British voice actors as opposed to the re-dubbed US version."
Phantasmagoria - Windows version available with superior FMV quality.
Pinball Gold Pack - Release has various issues, and it seems largely incomplete (read multiple posts).
Raptor, Call of the Shadows - Mountain King version of the game: Changes where made by mountain king to the soundtrack, the explosions and also the slowing down of the keyboard controls.
Rayman Forever - This version of the game is missing about half of the original's sound files.
Realms of Arkania - No soundtracks or redbook audio. Apparently, old installers had it.
Riven - CD-ROM version. Superior FMV quality DVD version is available.
Rollercoaster Tycoon Deluxe - US version with different names of rides vs. original UK.
Serious Sam Gold - This version had Dark Island expansion pack.
Sim City 2000 SE - Missing Windows version and no enhanced network play and interface from the Gold Edition.
The Incredible Machine - Forum thread. Some of these issues may be licensing related or missing titles that may be sold separately, but missing audio is never any good.
Space Quest - Missing the Space Quest 1 remake SCI version.
Wing Commander 1 + 2 - DOS versions. WC1 only has speech in Super Wing Commander. Wing Commander II has the speech pack. Missing Kilrathi Saga versions.
Wing Commander Privateer - CD Version. Using a different set of voice actors, the original version with speech pack only added voices to the introduction and during combat.
Zork: Grand Inquistor and Return to Zork: Reelmagic - Missing DVD version with high quality video.

Non-working / Needs patches removed or added

Chaos Overlords - Looping sound.
Corsairs Gold - Inaccesible Adventure Mode, Dutch and Polish versions of "The New Conquerors" expansion is broken
Divine Divinity - In game music is fixed, but check here for more bugs.
Dungeon Keeper 2 - RE-ADDED. It is still messed up.
Entomorph - Scrambled soundtrack.
Gangsters: Organized Crime - Problem with hoods getting stuck in jail forever. Caused by v1.4 patch.See here.
Gorky 17 - Broken graphics and videos abound, but here is a link for some fixes that seem to work for people.
Heroes of Might and Magic II - CD audio rips are bad. Must use FLAC OST and convert to OGG to fix them.
Little Big Adventure - Audio rips are bad.
Lords of Magic - Missing audio files.
Messiah - Unstable: check forum.
Raptor, Call of the Shadows - Soundtrack is encoded in garbage quality.
Seven Kingdoms 2 - Missing all the in-game music.
Tex Murphy: Overseer - and [url=http://www.gog.com/en/forum/tex_murphy_series/overseer_alcatraz_cell_block_crash]Link 2 - It seems like passing this bug is hit or miss, but for some people it's a major game breaker, which may make the game impossible to finish.
Tom Clancy's Ghost Recon - There is no way to install the expansion packs on the GoG version because GoG team (or UBI) pre-patched it too high.

Tom Clancy's Rainbow Six - Something with the rendering system causes invisible hostages, which makes a mission impossible to pass. Details, Alfie3000: " Apparently, It's caused by missing data files: Here & Here . And, it's also missing the in-game music entirely (It should play during certain parts like when a team member is killed.)"
Total Annihilation - By porting the soundtrack to MP3s, it broke in-game. It repeats tracks infinitely or does not immediately allow for turning the music off.
Tropico Reloaded - On netbooks without a disc drive, people are having trouble playing this w/o Daemon-tools or similar.
Worms 2 - Out of synch music in videos.

Games *JUST* Missing Expansion Packs

Alien Nations - Missing Alien Nations Mission Pack, but it's in Russian and German only.
American Conquest - Missing standalone expansion Fight Back and Divided Nation.
Arcanum - Official Modules.
Capitalism 2 - Missing Capitalism Lab.
Castles - Missing The Northern Campaign.
Cultures - Missing the expansion Cultures: Die Rache des Regengottes.
Descent I + II - This is not the Definitive Edition. Check the forum for links to download the remaining files for the Vertigo expansion, etc.
Disciples II - Rise of the Elves Gold - The previously mentioned "expansion" has its own Gold Edition that adds a new campaign and 4 more skirmish maps.
Duke Nukem 3D - Missing: Duke Caribbean, Duke It Out in D.C. and Nuclear Winter. STEAM has them.
FA 18 Super Hornet - Missing Albanian Campaign-mission disk.
Neverwinter Nights - Missing premium modules Pirates of the Sword Coast, Infinite Dungeons and Wyvern Crown of Cormyr.
Perimeter: Emperor's Testament - Missing standalone expansion.
POD Gold - This 'Gold' version of the game is missing the Back To Hell expansion.
Populous 1 - Missing the Final Frontier - Amiga ONLY.
Rainbow Six - Missing Eagle Watch.
Rayman - Aridoom: "(...) is missing the 60 Levels expansion. It was included in the French Rayman Collector compilation pack but English releases also exist (see Rayman Compilation.
Settlers: Heritage of Kings - Missing Expansion Disc and Legends Exp. Disc.
SpellForce 2: Faith in Destiny - Missing standalone expansion.
The Chronicles of Riddick: Assault on Dark Athena - Free DLC missing.
Tom Clancy's Ghost Recon - Missing Desert Siege and Island Thunder.
Tomb Raider 1 - Missing Unfinished Business.
Tomb Raider 2 - Missing The Golden Mask.
Tomb Raider 3 - Missing The Lost Artifact.

'Fixed' by GOG staff since thread inception and last edit:

Alone in the Dark 1-3 - Added missing newspapers and playing cards.
Battle Isle Platinum - Incubation and Wilderness were bugged versions.
Battle Realms - Manual added.
Betrayal in Antara - Go here to read about the problem. The game was broken.
Blood - CD audio rips fixed.
Broken Sword 1 - This had the original added to it!
Broken Sword 2 - It now includes the remastered version!
Conquest of the New World - It was missing the intro movie (~12 MB), but added in 04/2012.
Dark Fall 1 & 2 - Re-added back to GOG as Director's Cut versions. Now, Dark Fall: Lights Out has the original as well.
Dark Reign - Added "Dark Reign: Battles of the Outer Rim" expansion.
Dragonsphere - Added copy protection paperwork.
Dungeon Keeper - Added Deeper Dungeons.
Earth 2140 - The original GOG version was a later Windows release with broken AI. As of 02/2012, the DOS edition is available to download with correctly working A.I. New windows version available with possibly better A.I.
Entomorph: Plague of the Darkfall - Manual added.
Gobliiins - Both floppy and CD-ROMs are now available.
Hammerwatch - Linux version was missing the expansion Temple of the Sun + patch 1.3
Heroes of Might & Magic II - Now includes DOS + Windows version.
Incubation (Battle Isle Platinum Pack) ) - Added original manual.
King's Bounty - This game was bugged at release. Regardless of how GOG Team fixed the product, the game is now in working order.
Lesuire Suit Larry Collection - SVGA part 6 added.
Lords of the Realm Royal Edition - Added the CD-ROM version with cinematics and redbook audio. Also, CD-ROM had game map selection between England and Germany.
Magic Carpet - Added Hidden Worlds.
Masters of Magic - Added Advances Chart.
Might & Magic I-VI LE - Added CD versions of Might & Magic 4 and 5 (Worlds of Xeen) with full voice acting for all the NPCs. New map added for M&MII.
Moto Racer 2 - The game's copy protection no longer interferes with gear-shifting.
Pinball Gold Pack - Audio tracks added and fixed.
Police Quest - AGI version added.
Populous 1 - Added The Promised Lands.
Populous: The Beginning - Added Undiscovered Worlds.
Pro Pinball: Timeshock - Added Windows version, making the game playable.
Rayman Forever - Although, this version does not have an intro movie, the GoG staff has added the movie as an extra download.
realMyst - Manual added.
Sid Meier's Alpha Centauri - Added Alien Crossfire.
Silent Storm Gold - New installer version fixing various glitches.
Soldiers: Heroes of WW2 - Back in stock.
Syndicate - Added American Revolt.
Tex Murphy Overseer - OST added. Version 2.0 has the superior video quality DVD version.
Tex Murphy: Pandora Directive - Manual added.
Ultima IV - Spellbook scan was missing page 8. Player reference card was missing.
Wing Commander Titles - Added WCI and II expansions.
Wing Commander: Privateer - Added Righteous Fire. Still CD Version with full speech.

*NOTE: GOG fixes or adds items that are not included on this list.

'Fixed' by GOG community since thread inception and last edit:

Entomorph: Plague of the Darkfall - Manual added.
Dungeon Keeper 2 - Recruitment bug.
Witcher - Fix Bink32.dll issues and more here.
Interstate '76 - A big thank you to the community for the fixes.
Psychonauts - Patched to latest version.
Realms of The Haunting - GOG version is the original UK edition and cannot have key-binding changes made, which can be corrected by the game to the US version. Also, it's missing a [url=http://www.gog.com/en/forum/realms_of_the_haunting/gog_should_replace_the_uk_version_with_the_us_version_of_the_game]few other minor tweaks.
Two Worlds - NPCs lip-sync fix.

If a game does not work, then file a product support case. GOG team doesn't check the forums enough. In addition, from their response to one person from the I76 thread, they base how well a game is actually working for us by how many support cases are filed by us.

Why did you create a new thread? What's wrong with the old one?

The character limit. Even if I grammatically clean it up, I couldn't add anything else. So, I am discontinuing that thread to make more space. It's easier for the information to be consolidated in one area in the first few posts than weeding thru page after page, so this was my best option.

*favourited*
Check the last page of the previous thread. Earth 2140 is shipped with dead AI.
Also, you can add some details now. Make a correction for Battle Isle, Incubation the bugged game in the package.

Ultima 4 player reference card oddly enough is included into Ultima 4+5+6 package.

Wing Commander: Privateer and Sid Meier's Alpha Centauri are also missing their exapansions.

Instead of quoting me about 2140, you could link to this thread
http://www.gog.com/en/forum/earth_series/open_letter_remove_the_broken_version_of_earth_2140_from_catalogue_gog/page1

Syndicate: missing American Revolt expansion
Wing Commander I: missing The Secret Missions 1+2
Wing Commander II: missing Vengeance of the Kilrathi (Special Operations 1+2)
Populous 1: missing The Promised Lands and the Final Frontier
Magic Carpet: missing Hidden Worlds
Rainbow Six: missing Eagle Watch

Republic: The Revolution is sold through Eidos online store.

Maybe it will resurface now that SE is on board.

Why so many games missing expansions?
Publisher restrict GOG to release games as vanilla?
Those expansion have not been sold any other place without used,and so far we have no solely expansion item in GOG store.
It's mystery.

Minor adjustments for back-up purposes

Settlers 2: Gold Edition - Manual is not in the installer. It can be found under additional content.

Just about every EA game (with, I think, an exception or two) came without expansions. GOG hasn't stated the reason, we only ever get generic "We're working on the issue" messages.
While I personally don't mind the lack of expansions, especially if they'll EVER get added to the games, many are outright furious about the issue, so I guess the staff's doing everything in their power to fix it, but it's been like this since EA came to GOG.

Bookmarked, thanks for this thread :) Btw how did you post 3 times?