very good catch!

added Silent Hunter series

added Hammer & Sickle

removed Magic Carpet 2: The Netherworlds
removed The Settlers III
removed The Settlers III: Quest of the Amazons
added The Settlers IV: Mission CD
added SimCity (2013)
added Tomb Raider (2013)

added Catacomb series

added The Guild series

added The Settlers: Heritage of Kings - Expansion Disc
added The Settlers: Heritage of Kings - Legends Expansion Disc

removed Syndicate Wars

removed KKnD series

My 'Strike commander should be considered a Wing Commader spin-off' OCD has cleared right up now its been added (with all expansions and speech packs too, which is awesome) so that good too!

Arma 3 :(

The Desperados series is missing its third chapter: Helldorado
http://www.mobygames.com/game/windows/helldorado

The Rise Of The Triad series is missing The Hunt Begins (Deluxe Edition), a shareware version of Rise Of The Triad, consisting of ten brand new single player levels and eight multiplayer maps, all exclusive to the shareware version, the Deluxe Edition boasts an additional three single player levels and three multiplayer maps.
http://www.mobygames.com/game/rise-of-the-triad-the-hunt-begins
http://www.mobygames.com/game/rise-of-the-triad-the-hunt-begins-deluxe-edition

Rise Of The Triad is also missing Extreme Rise Of The Triad, a forty two levels add-on made by Apogee.
http://www.mobygames.com/game/extreme-rise-of-the-triad

Alien Nation is missing its Mission Pack
http://www.mobygames.com/game/windows/alien-nations-mission-pack

The Alien Shooter series seems to be missing a bunch of titles and upgraded versions, which ones and how many is hard to ascertain as Mobygames' page for the series seems to be incomplete and the developer' official website lists a lot more Alien Shooter titles.
http://www.mobygames.com/game-group/alien-shooter-series
http://www.sigma-team.net/games/index.html

The Enemy Engaged series (Apache Vs Havoc, Comanche Vs Hokum) are missing Enemy Engaged 2 and its add-on, Desert Operations
http://www.mobygames.com/game/enemy-engaged-2-gold-edition

Cryo's Atlantis series is missing the last two games: Atlantis Evolution and Secrets Of Atlantis
http://www.mobygames.com/game/atlantis-evolution
http://www.mobygames.com/game/secrets-of-atlantis-the-sacred-legacy

The Avernum series is missing the first game's recently released remake: Avernum: Escape From The Pit
http://www.avernum.com/avernum/

Can someone confirm if Battle Isle Platinum includes the Hidden World's ten exclusive Instant Action maps for Incubation?
http://www.mobygames.com/game/incubation-hidden-worlds

The Krondor series is missing Betrayal in Antara and Return To Krondor
http://www.mobygames.com/game/betrayal-in-antara
http://www.mobygames.com/game/raymond-e-feists-return-to-krondor

A quick look at the Blitzkrieg series page on Mobygames seems to indicate that many add-ons are missing on GOG, someone that owns the GOG versions and who is knowledgeable in the series and its many expansions could surely tell us more.
http://www.mobygames.com/game-group/blitzkrieg-series

The third Bloodrayne game is missing
http://www.mobygames.com/game/bloodrayne-betrayal

The Combat Mission series is missing a bunch of titles
http://www.mobygames.com/game-group/combat-mission-series

Although it does not exist in my heart, the Commandos series is missing Strike Force
http://www.mobygames.com/game/commandos-strike-force

This was me posting to add Helldorado and Rise Of The Triad, getting derailed and ending up wasting the better part of my evening and only managing to go through the letters # to C of the entire game list. Someone else, feel free to crosscheck letter D and onward on Mobygames and Wikipedia, I think I've given enough for tonight.

The Third Bloodrayne game was only released on consoles.

Thanks for this wonderful post, very helpful. I will check each one of your suggestions
added Helldorado
I had added the above before but it has been suggested that the missing missions are already included in the gog version. Please check pages 5-7 of this thread. Let me know if you still believe something is missing
added Alien Nations Mission Pack

gog page says:

"What's cool about it:
The pack includes the original Alien Shooter and its expansions Alien Shooter: Fight for Life and Alien Shooter: The Experiment
A unique pack of the legendary Alien Shooter with all add-ons in existence!"

I am not sure what exactly is missing here. Anyone owns Alien Shooter games?
added Enemy Engaged 2
added Enemy Engaged 2: Desert Operations

Seems like it is missing three games.

added Curse of Atlantis: Thorgal's Quest
added Atlantis Evolution
added The Secrets of Atlantis: The Sacred Legacy
added Avernum: Escape from the Pit
awaiting confirmation