I would like to see a list of games on GOG that have mods/mod tools/source available, particularly if the list can be verified as to whether the version sold on GOG is capable of supporting the mods.
To start, here are the games from the GOG list that I know have mod tools.source available (although whether said tools/source will work with the GOG versions I cannot say):
Neverwinter Nights (had an official level editor)
Blood 2 (had a limited source release of just the game code whilst the engine remains proprietary)
Call to Power 2 (had a full source release minus the 3rd party libraries if I remember correctly)
Dark Reign (had an official map editor/set of mod tools)
Dark Reign 2 (I think it had a map editor, also the source code is out there if you google for it, not sure if the source is an official release or a leak though)
Descent series (I know a number of these had source releases and/or tools but I haven't followed the series enough to know for sure which ones)
Duke Nukem 3D (had a source release)
Empire Earth (definatly map editors and mod tools for these)
Heroes of Might and Magic (I know that HOMM2 at least had a map editor)
Rise of the Triad (had a source release)
Rollercoaster Tycoon (definatly moddable, I should know, I WROTE the first mod tools for RCT3 back in the day :)
Simcity 2000 (this had tools that let you create new building artwork for the game)
Unreal (I am 99% sure tools exist for all of these and I do know that modding helped make the Unreal series the success it is today)

Maybe others can take it from here and identify other games on the GOG list that are capable of being modded or that have source available and can verify whether the GOG versions are compatible with the mods/tools/source that exist for these games.

I haven't seen a thread like this before, if what I am posting has been posted before (or is something that shouldn't be posted but should be handled through some other way) please feel free to let me know :)

Sacrifice has Scapex, where you can make maps and campaigns and stuff, but I never used it.

Arx Fatalis had source release, and a source port

There is a distinct lack of Jagged Alliance 2 in your list. All 3 JA2 games (JA2, JA2: Unfinished Business and JA: Wildfire) have all had their sources released, though I'll have to go look for them, especially the WF one.

Edit: I can't find a link for JA2:WF source code, so it is possible that it hasn't been released. JA2 and JA2:UB do have their source released though, and JA2:UB also has a map/mission editor.

ARMA II: Combined Operations has both a level editor and can be fully modded with guns, vehicles etc. and has a very good and alive mod community.

Shadow Warrior had its source code released.

What applies to Neverwinter NIghts, also applies to <span class="bold">Neverwinter NIghts 2</span>.

And <span class="bold">The Witcher</span> is based on the same engine as NWN and also allows to create and play user-made adventures.

Blades of Avernum (part of Avernum: The Complete Saga) comes with a scenario editor and has fan-made mods available. I don't own the GOG version, but I'd be very surprised to hear that there are compatibility issues (I really doubt it).

Same goes for <span class="bold">Driftmoon</span> which was explicitly made with modability in mind.

<span class="bold">Torchlight</span> includes an editor; the GOG version didn't support mods on release, but that was fixed soon after.

The Dungeon Editor for <span class="bold">Legend of Grimrock</span> is part of the GOG package, too.

I hear <span class="bold">The Temple of Elemental Evil </span> is a lot better with the inclusion of mods, specifically the Circle of Eight modpack.

You can also find mods for <span class="bold">FTL: Faster Than Light</span>.

I'm not sure if it's really modable and to what extent, but <span class="bold">Zafehouse Diaries</span> at least allows you to customize characters and places by adding your own photos or images.

Also, I just remembered this thread that might contain references to the occasional GOG game, too (although quite a few of these games currently aren't on GOG). :)

Well, UB has been ported to 1.13 with varying degrees of success, but I haven't really tested it. Grab one of the newer SCIs by DepressivesBrot and you should have a working copy. Do ask if you want more info, though I won't be able to reply for ~10 hours.

Yep, that is the Urban Renewal Kit which is included in the Special Edition here on GOG. I remember playing around with it back when it was originally released. I never did much with it because I sucked at art, but used it to import other people's graphic sets into the game.

This site has some nice user-generated building graphics:
http://www.sc3000.com/sc2000/scurk/

http://www.gog.com/forum/general/gog_source_ports

There you go :) Add to it if it needs it :)

The Blake Stone games...
Rise of the Triad: Dark War

With hundreds of FMs and a few total conversions, Thief (1. 2. and 3) is moddable ;)

Do you mind if I ask another JA2 related question? Is there any reason (given the source is available) that JA2/expansions have never gotten resolution mods similar to how games like Baldur's Gate/Fallout got them, to expand the size of the map shown to widescreen resolutions?

What do you mean? 1.13 can be played in up to 2560x1600 resolution, though that is done by increasing the view area in the tactical map. As for the strategic map, that requires to create a proper image, so far there are images for 640x480 resolution, 800x600 and 1024x768. Not sure if there is anyone still working on that though, but higher resolutions (including widescreen) should be available in Brot's SCI.