Cyber Hook is missing the "Lost Numbers DLC".
Blue Fire is missing the level editor "Void Maker".
Source of Madness is missing the soundtrack / Nightmare Edition.
Legend Bowl is missing the soundtrack.
Recursive Ruin is missing the soundtrack.
Curious Expedition 2 is missing the soundtrack.
Abandon Ship is missing the soundtrack.
Paradise Killer is missing the Art of Paradise DLC (artbook).
My Time At Portia is now missing also the Mac build,
Player Costume Package DLC,
NPC Eveningwear Package DLC.
Out There: Oceans of Time is missing the Celestial Edition,
Soundtrack DLC,
Wallpapers DLC,
Deluxe Skins DLC.

According to messages on their pages, DEFCON and Multiwinia lack 64-bit builds for macOS, however these were released on Steam, and also on the now-deleted websites for these games. Since the files for these games were distributed publicly, it may be possible to find them in the Wayback Machine.

STAR WAR Knights of the Old Republic™ II: The Sith Lords
Has finally received the patch that was missing from 2015

Source: https://www.gog.com/forum/general/the_what_did_just_update_thread/post27994

Curse of the Dead Gods is missing paid soundtrack DLC.

Dawn Of The Monsters doesn't have the achievements.

Missing achievements are tracked in the List of broken GOG Achievements thread. Dawn of the Monsters is already listed as missing 30 achievements.

Maybe the patch had a critical bug? Anyone knows?

As far as we're concerned, too damn many, and we make a point, where possible, of calling out the devs on their Discord forum, then wait for their lame reply, if they even bother to offer one. As a result, our rating of their product , here, as well as on Ste*m, is downgraded accordingly. Shoddy support; shoddy review.

Starpoint Gemini 2 is missing Collector's Upgrade DLC.

Worms: Armageddon. The digital release, both Steam and GOG, lacks some content, restored by an unofficial patch.

If the GOG version is the same as the other stores then it is not a 2nd class citizen.

Thank you for the information.
Even if sadly, people won't add it to the doc, for the reason alexandros050 explained.

Retail box not being a store?

The Elder Scrolls IV: Oblivion - Game of the Year Edition Deluxe (addition, uncertain). On Steam, it has additional languages, however the edition with more DLCs is said to be English-only anyway.