UPDATE

GOG locked an old thread that no one touched for one month.
https://www.gog.com/forum/general/list_of_drmfree_video_games_digital_distributors

The thread is over 4 years old.
The thread helped a lot of people to find DRM-free stores.
GOG just punished me because I hope them let Russians and Belarusians buy DRM-free games.
Fuck you GOG. I will never spend any money here.

And I will stop to update my threads.

Note: games that directly compatible with ScummVM and DOSBox are not listed in this thread.

Compatible with Amiga emulators
Defender of the Crown~
Rocket Ranger~
Wings~

~ Extract adf files with winrar

Compatible with Apple II emulators
The Bard's Tale (1985)
The Bard's Tale II: The Destiny Knight
The Bard's Tale III: Thief of Fate

Compatible with Apple IIgs emulators
Nox Archaist^ (HOWTO)
The Bard's Tale (1985)^
The Bard's Tale II: The Destiny Knight^
The Bard's Tale III: Thief of Fate^

^ Run Apple IIgs version in MESS

Compatible with Commodore 64 emulators
MicroProse Soccer (DOS versions is also available)
Super Huey™ 1 & 2 Airdrop

Compatible with Famicom/NES Emulators
Jim Power The Lost Dimension
Konami Collector's Series: Castlevania & Contra
SNK 40th Anniversary Collection (HOWTO) Compatible with Game Boy Emulators
Disney Classic Games Collection (HOWTO) (Includes Game Boy, SNES and Mega Drive / Sega Genesis ROMs.)

Compatible with Mega Drive / Sega Genesis Emulators
Disney Classic Games Collection (HOWTO) (Includes Game Boy, SNES and Mega Drive / Sega Genesis ROMs.)
Jim Power The Lost Dimension
Switchblade
TANGLEWOOD
The Second Samurai
Water Margin

Compatible with NeoGeo Emulators
ART OF FIGHTING 2*
BASEBALL STARS 2*
BLAZING STAR*
FATAL FURY SPECIAL*
GAROU: MARK OF THE WOLVES*
IRONCLAD*
KING OF THE MONSTERS*
METAL SLUG*
METAL SLUG 2*
METAL SLUG 3*
METAL SLUG X*
NEO TURF MASTERS*
PULSTAR*
REAL BOUT FATAL FURY 2: THE NEWCOMERS*
SAMURAI SHODOWN II*
SAMURAI SHODOWN V SPECIAL*
SENGOKU 3*
SHOCK TROOPERS*
SHOCK TROOPERS: 2ND SQUAD*
THE KING OF FIGHTERS 2000*
THE KING OF FIGHTERS 2002*
THE LAST BLADE*
THE LAST BLADE 2* (Needs neogeo.zip from other games)
TWINKLE STAR SPRITES*
SNK 40th Anniversary Collection (HOWTO) * Playing SNK releases in OpenEmu

Compatible with Sega Mark III / Sega Master System Emulators
Wonder Boy: The Dragon's Trap (HOWTO)

Compatible with Super Famicom / SNES Emulators
Disney Classic Games Collection (HOWTO) (Includes Game Boy, SNES and Mega Drive / Sega Genesis ROMs.)
Iron Commando
Jim Power The Lost Dimension
Legend
Street Racer (DOS versions is also available)
The First Samurai
Zombies Ate My Neighbors and Ghoul Patrol (HOWTO)

Compatible with MAME
Bad Dudes
Double Dragon 1, 2, 3 (HOWTO)
Express Raider
Gate of Doom
Heavy Barrel
Joe & Mac - Caveman Ninja
Joe & Mac Returns
Night Slashers
Raiden Legacy$
SRD - Super Real Darwin
Super BurgerTime
Two Crude
Wizard Fire

$ Use the Python 3 script provided by renloz

Compatible with Nintendo Switch
Aquaria (HOWTO)

Compatible with PlayStation Emulators
Shadow Madness

Compatible with PSP
Aquaria (HOWTO)

Compatible with ScummVM (Extracted resources from remastered games)
(Listed at #3 due to forum limitation)

GOG games that contains disk/disc image(s)
(Listed at #3 due to forum limitation)

The Bard's Tale (2004) contains emulated versions of the classic games. Once you have started any of those games, you can then take the disk images and run them in an emulator. I believe MESS (which I believe is part of MAME) will work (but note that these games expect a keyboard instead of a controller).

Compatible with ScummVM (Extracted resources from remastered games)
Day of the Tentacle (1993) and Maniac Mansion Enhanced Version (1989) (HOWTO)
Full Throttle (1995) (HOWTO)
Monkey Island 2: LeChuck's Revenge (1991) (HOWTO)
The Secret of Monkey Island (1990) (HOWTO)

GOG games that contains disk/disc image(s):
Albion DOS iso
Alone in the Dark: The Trilogy 1+2+3 All parts: DOS and Win 3x iso
Archimedean Dynasty (Schleichfahrt) DOS iso
Biing!: Sex, Intrigue and Scalpels
Carmageddon Max Pack Carmageddon and Splat Pack DOS iso
Dark Sun: Wake of the Ravager
Dragonsphere DOS iso
Gabriel Knight: Sins of the Fathers DOS and Win 3x iso
Humans 1
Humans 3: Evolution Lost in Time
Menzoberranzan
Normality DOS iso
Pinball Dreams
Pinball Fantasies
Pinball Illusions
Pirates! Gold Plus Pirates! Gold DOS iso
Police Quest: SWAT 1+2 Daryl F. Gates Police Quest: Open Season (Police Quest 4) DOS iso
Quake: The Offering Quake: Windows iso, Mission Pack 1 DOS and Win iso, Mission Pack 2 DOS and Win iso
Ravenloft: Stone Prophet
Ravenloft: Strahd's Possession
Rayman Forever DOS iso
Realms of Arkania III: Shadows over Riva DOS iso
Sensible World of Soccer 96/97 DOS iso
STAR WARS: TIE Fighter Special Edition DOS iso (in Collector's CD-ROM edition)
STAR WARS: X-Wing Special Edition DOS iso (in Collector's CD-ROM edition)
System Shock DOS iso CD and Floppy in Classic Edition
Teenagent DOS iso
Worms United DOS iso
X-Com: Apocalypse DOS iso

Nvm, i need to take some coffee, still sleeping it seems.

METAL SLUG 3 do have macOS and Linux files in GAME GOODIES section.

Yep you're right, i just doublechecked and the files are there. Seems i hadnt download the extras for MS 3 and assumed it hadnt any like some of the other titles.

I have no idea.

UPDATE
ART OF FIGHTING 2
GAROU: MARK OF THE WOLVES
IRONCLAD
NEO TURF MASTERS
PULSTAR
REAL BOUT FATAL FURY 2: THE NEWCOMERS
SENGOKU 3
SHOCK TROOPERS: 2ND SQUAD

MAME is both MAME and MESS now (the two projets merged around 2015), is still called MAME.

Nice thread, thank you :)
Only full copies of the games (ie usable without specific emulators / launchers) are actually 100% DRM-free.

I changed the subtitle a bit for MAME/MESS, thank you!
I guess those ROMs are compatible with many different emulators, but need someone to test them and report it.
Since they are compatible with GOG's emulator, and at least other one emulator, it is good enough for me.
At worst situation, I still have two emulators for each game. :-P

No worries, when I wrote "specific" I meant "the one provided by GOG" but that was unclear ;)

Push this thread for Monkey Island and Maniac Mansion series.

Unconfirmed
THE KING OF FIGHTERS '98 ULTIMATE MATCH FINAL EDITION

Wonder Boy: The Dragon's Trap includes the ROM of the original version of the game; the file name is wb3.sms

ADDED, thank you!