Quite a large one too.
A little background: At first there was no good compiled source of information as to what mods are worthwhile to check out, and googling for mods is often a fool's game. GOG's forums used to be pretty unorganized, so while good information could be found there, you usually had to go through a ton of threads to find it (hence the need for an organized list). They've really been on top of the ball since then, and have stickied useful posts for each game about the game's mods. We almost don't need a reference for the mods anymore, but it's a neat little list, and fills in a couple things you might not catch (GOG doesn't have everything stickied).
So, first, here's a list of game updates I noticed while running through the titles:
Battle Isle: New build with additional hotfixes built in
Duke Nukem Manhattan Project: New build with Prism3D error hotfix built in
Gabriel Knight 2: New build with better sound, interlaced video patch/fix, misc fixes
Heroes of Might & Magic II Gold Edition: New build with patch 2.1 fixes & improved implementation of PoL
IL 2 Sturmovic 1946: New build with official patch 4.1
Incoming Forces: New build with cd audio music
Realms of Arkania 1 + 2: New build, fixes sound problems, adds VA in cutscenes and full intro for RoA2
Septerra Core: Legacy of the Creator: New build, fixes skipping dialog problems
These are games that have been re-compiled in to a newer .exe accessible from your account page (so re-download them if you got them around release).
Then we have a summary of newly added games with MODs / games with changes:
Arcanum: added Beta Content Restoration Pack
Arx Fatalis: added game, performance patch
Baldur's Gate 1/2: cleaned up, added mods, BiG World v10 out
BloodRayne 2: added game, FSAA + high-res texture pack
Colin McRae Rally 2005: added game, Group B car improvements, unlock all, extraction tools
Descent 1 & 2: added game, DXX-Rebirth mod (newer version just released), high resolution + improved graphics and joystick support
Die by the Sword: DBTS Extended updated (engine replacement), added other mods
Duke Nukem 3D: High Resolution Pack / eduke32 updated
Earth 2150 & Earth 2160: added game, balancing mods + misc others
Enemy Engaged: Comanche vs Hokum: added game, large mod pack improves graphics + more
Evil Genius: added game, UOP v1.1, adds high-res/widescreen & other fixes
Fallout: Added FIXT, all-in-one patch. Updated & cleaned up section.
Fallout 2: Updated & cleaned up section.
Fallout Tactics: New mod link / guide
Far Cry: New link, FCAM updated (all-in-one mod, fixes everything, high res textures, etc etc)
Freespace 1 & 2: Cleaned up section, new links to FSO, SCP, Upgrade Project, & FSP
Ghost Master: added game, widescreen fix
Giants: Added link for new (almost released) UOP 1.5
Gothic: New Unofficial Patch, cleaned up section
Heroes of Might & Magic II: Added Free Heroes 2 mod (high res support + new features)
Heroes of Might & Magic III: Added HoMM3 HD mod (high res support + new features), Horn of the Abyss
Heroes of Might & Magic IV: Added game with Equilibris mod (rebalance / fixpack)
Icewind Dale 1 & 2: Cleaned up sections
Master of Magic: Added game, Insecticide Patch (fixes bugs, improves AI & UI)
MDK: Added game, WASD + Mouse config
Might & Magic VI: GrayFace MM6 Patch v1.10 (adds always run, quick saves, changing controls, mouse look, etc)
Might & Magic 7: Added game, GrayFace MM7 Patch v1.5.1 (adds always run, quick saves, changing controls, mouse look, etc)
Might & Magic 8: Added game, GrayFace MM8 Patch v1.4 (adds always run, quick saves, changing controls, mouse look, etc)
Moto Racer: Added game, command line tweaks (including framerate cap removal)
Operation Flashpoint: Added game, widescreen fix, various mods
Postal: Fix for left turn & spinning NPCs
Prince of Persia: Sands of Time: Added game, widescreen / highres fix
Rayman 2: Added game, edit .ini for additional resolution support
Sensible Soccer 2006: Added game, mega patch & other mods
Sid Meier's Alpha Centauri: Added game, SMAC 444 (AI patch) & widescreen tweak
The Witcher: Added game, mod list & troubleshooting
The Witcher 2: Added game, mod list
Vampire The Masquerade - Redemption: Added game, Souls In X-ile Mod
Large enough update that I've had to split it to two posts! Here they are (and also easily accessible in the OP):
MOD INFO A-M
MOD INFO N-Z
Should be more useful now too, as it's much more up to date.