Following kbnrylaec's decision to no longer update the ROM based GOG games compatible with third party emulators thread I have decided to create a new tracker for games with obtainable ROMs that you can buy on GOG. I will also add instructions on how to extract these ROMs where applicable.

A lot of the links below build on kbnrylaec's work and I would like to give my thanks for the time spent compiling this list. I will do my best to maintain and add to it for everyone's benefit, since I am going to follow up on it for my own retro gaming enjoyment.

Note: I will NOT be tracking either DOS or ScummVM-compatible games on this thread.

I can recommend using RetroArch and its many backend libretro cores to play these games, but if that seems too daunting and you're looking for an easier solution (although, sadly, not available on Windows)...
hit up RetroPie.

Here's the current list:

Compatible with Mega Drive / Sega Genesis emulators
Brave Battle Saga - The Legend of The Magic Warrior
Contra Anniversary Collection (HOWTO) (Includes Game Boy, NES, SNES and Mega Drive / Sega Genesis ROMs.)
Disney Classic Games Collection (HOWTO) (Includes Game Boy, SNES and Mega Drive / Sega Genesis ROMs.)
Jim Power - The Lost Dimension
Switchblade
TANGLEWOOD
The Gadget Twins
The Second Samurai
Water Margin - The Tale of Clouds and Wind
Zero Tolerance

Compatible with Super Famicom / SNES emulators
Contra Anniversary Collection (HOWTO) (Includes Game Boy, NES, SNES and Mega Drive / Sega Genesis ROMs.)
Disney Classic Games Collection (HOWTO) (Includes Game Boy, SNES and Mega Drive / Sega Genesis ROMs.)
Dragonview
Gourmet Warriors (aka Gourmet Squad / Gourmet Sentai Bara Yarou)
Iron Commando
Jim Power - The Lost Dimension
Legend
Radical Rex
Street Racer
Soccer Kid
Super 3-D Noah's Ark
Tinhead
The First Samurai
Zombies Ate My Neighbors and Ghoul Patrol (HOWTO)

Compatible with NeoGeo emulators (see Playing SNK releases in OpenEmu)
3 COUNT BOUT *
ALPHA MISSION II *
ART OF FIGHTING 2
ART OF FIGHTING 3: THE PATH OF THE WARRIOR *
BASEBALL STARS 2
BLAZING STAR
CROSSED SWORDS *
FATAL FURY SPECIAL
GAROU: MARK OF THE WOLVES
GHOST PILOTS *
IRONCLAD
KING OF THE MONSTERS
KING OF THE MONSTERS 2: THE NEXT THING *
KIZUNA ENCOUNTER: SUPER TAG BATTLE *
LAST RESORT *
MAGICIAN LORD *
METAL SLUG
METAL SLUG 2
METAL SLUG 3
METAL SLUG X
MUTATION NATION *
NEO TURF MASTERS **
NINJA COMMANDO *
NINJA MASTER'S：HAOH NINPO CHO *
OVER TOP *
PULSTAR
REAL BOUT FATAL FURY 2: THE NEWCOMERS
ROBO ARMY *
SAMURAI SHODOWN II
SAMURAI SHODOWN IV: AMAKUSA'S REVENGE *
SAMURAI SHODOWN V SPECIAL
SENGOKU *
SENGOKU 2 *
SENGOKU 3
SHOCK TROOPERS
SHOCK TROOPERS: 2ND SQUAD
SOCCER BRAWL *
SUPER SIDEKICKS *
THE KING OF FIGHTERS '97 (GLOBAL MATCH) *
THE KING OF FIGHTERS 2000
THE KING OF FIGHTERS 2002
THE LAST BLADE
THE LAST BLADE 2 *
THE SUPER SPY *
TOP HUNTER: RODDY AND CATHY *
TWINKLE STAR SPRITES
SNK 40th Anniversary Collection (HOWTO) * Code Mystics releases, use this guide to extract the ROMs. As of now ROMs for THE KING OF FIGHTERS 2003 and METAL SLUG 4 can't be extracted due to these releases containing a combination of assets from multiple ROM sets (assembling a single compatible set is challenging).

** No longer sold on GOG

Note: Newer versions of some of the DotEmu releases of NeoGeo titles no longer pack a ready-to-use ROM file. Fallback to the Linux installers (available as goodies) and unzip them to get the ROMs in these cases.

Compatible with Arcade emulators (MAME)
Bad Dudes **
BreakThru **
Double Dragon 1, 2, 3 (HOWTO)
Express Raider (also includes a ROM for Shootout) **
Gate of Doom **
Heavy Barrel **
Joe And Mac - Caveman Ninja **
Joe And Mac Returns **
Night Slashers **
Raiden Legacy (HOWTO)
Realms of Antiquity: The Shattered Crown (HOWTO)
SRD - Super Real Darwin **
Super BurgerTime **
Two Crude **
Wizard Fire **
Atari 50: The Anniversary Celebration (HOWTO) Compatible with PlayStation emulators
40 Winks
Glover
Motor Mash (HOWTO - audio track fix)
Shadow Madness
Tunnel B1

Compatible with Commodore 64 emulators
MicroProse Soccer
Super Huey 1 + 2 Airdrop
The Making of Karateka (HOWTO)

Compatible with Apple II emulators
Nox Archaist (HOWTO)
Phantasie II
The Bard's Tale III: Thief of Fate
The Making of Karateka (HOWTO)

Compatible with Apple IIgs emulators
The Bard's Tale (1985)
The Bard's Tale II: The Destiny Knight

Compatible with Amiga emulators
Another World (ROMs included in Extras, also see this post)
Defender of the Crown (HOWTO)
Rocket Ranger (see above HOWTO)
Wings (see above HOWTO)

Compatible with PC Engine / TurboGrafx-16 emulators
Impossamole

** No longer sold on GOG

Compatible with Atari 800 emulators
The Making of Karateka (HOWTO)
Atari 50: The Anniversary Celebration (HOWTO) Compatible with Atari 2600 emulators
Atari 50: The Anniversary Celebration (HOWTO) Compatible with Atari 5200 emulators
Atari 50: The Anniversary Celebration (HOWTO) Compatible with Atari 7800 emulators
Atari 50: The Anniversary Celebration (HOWTO) Compatible with Atari Lynx emulators
Atari 50: The Anniversary Celebration (HOWTO) Compatible with Atari Jaguar emulators
Attack of the Mutant Penguins
Atari 50: The Anniversary Celebration (HOWTO)

Compatible with Famicom/NES emulators
8 Eyes
A Boy and His Blob Retro Collection
Alwa's Awakening The 8-Bit Edition (the game is a DLC of Alwa's Awakening, so you will need both to get access to the ROM)
Contra Anniversary Collection (HOWTO) (Includes Game Boy, NES, SNES and Mega Drive / Sega Genesis ROMs.)
Disney Classic Games Collection (HOWTO) (Has the NES version of The Jungle Book)
Jim Power - The Lost Dimension
Konami Collector's Series: Castlevania + Contra (HOWTO)
Nightshade
Power Punch II
SNK 40th Anniversary Collection (HOWTO) Compatible with Sega Mark III / Sega Master System emulators
Wonder Boy: The Dragon's Trap (HOWTO)

Compatible with Game Boy emulators
A Boy and His Blob Retro Collection
Contra Anniversary Collection (HOWTO) (Includes Game Boy, NES, SNES and Mega Drive / Sega Genesis ROMs.)
Disney Classic Games Collection (HOWTO) (Includes Game Boy, SNES and Mega Drive / Sega Genesis ROMs.)

Compatible with Game Boy Advance emulators
Iridion 3D
Iridion II

While I am aiming to maintain this thread for any newly added titles, it may be the case I will not always purchase new retro releases. If you feel that anything is missing from the list, I'd appreciate your hints and contributions, as was the case in the past on kbnrylaec's thread. Thank you, and happy retro gaming! Thank you! Everything you mentioned should be added/corrected, if I understood correctly.

There seems to be at least a preliminary way to extract the ROMs from the Atari 50: The Anniversary Celebration collection.

Following the instructions in the link above, you will get a output.zip file that, when extracted, will contain a roms folder. Most roms present here can be outright used with available emulators, whereas arcade ROMs will need further conversion to work with MAME. AFAIK a way to convert them is not yet available, but I'll see if I can dig something up from previous Atari collections perhaps.

I'll gradually add a full list of extracted titles to the list above, so watch this space.

I was able to get some of the ROMs in the Arcade subfolder of the above mentioned roms folder by adapting an existing ROM extraction script for the Atari Vault.

See here for more details: https://gist.github.com/WinterSnowfall/7d87ed156fb65896fdba6e925e54bb2a

With the above you can extract and play the following arcade titles in MAME 2003:
- Asteroids
- Asteroids Deluxe
- Missile Command (loads with warnings, but appears playable)
- Tempest

Sadly, there are way more ROMs in that folder, but I'll leave it to the experts to eventually get them all.

Nice.

https://www.gog.com/game/gourmet_warriors

Gourmet Warriors

The rom is a file named game. I don't remeber in what folder it is, but just rename with the .sfc extension.

Oh, nice - a SNES game then. Thanks for the heads-up! I'll look at the retro games added today and update the list for sure :).

Edit: Alright, quite a few additions today, 3 new SNES games, two new PSX games and to top it all the first PC Engine ROM available on GOG! I just wish it was a better one like... Bomberman. But it's a start at least.

For anyone trying to play Motor Mash with the beetle-psx emulator, note that for some reason the .cue file included with the GOG version, although readily available, is missing audio track pregap info on all but the first audio track (track 2), which is causing all the other music tracks to loop erratically.

To fix this, one must copy: PREGAP 00:02:00 under all the audio tracks listed in the .cue file, and then subtract that value from the INDEX 01 time entry. This will skip the first 2 seconds of silence at the start of each audio track and ensure the emulator interprets them correctly.

For example:
TRACK 03 AUDIO
INDEX 01 09:05:43

will become:
TRACK 03 AUDIO
PREGAP 00:02:00
INDEX 01 09:03:43

The same thing has to be done for tracks 4 to 14 (track 2 is already correct).

The GOG release of Soccer Kid contains both the MS-DOS and SNES versions.

Thank you! I've added it to the list.

The Piko bundle that got released today contains 3 games with readily available ROMs that got added to the tracker, namely:

The Gadget Twins - Sega Genesis
8 Eyes - NES
Power Punch II - NES

The remaining 3 titles, while having PlayStation versions, do not include the PSX disc images, sadly.