I have no idea whether it's any good, but there's apparently an Amiga game called "Arabian Nights" that is not related to the Windows game.

(Of course, adding that game to the GOG catalog could create some game name confusion, so one of the games would need to be renamed for the purpose of GOG's version having a distinct name.)

Arabian Nights ist one of the best Platformer games on the Amiga, besides Mr. Nuts (which was a great port for the Amiga) and Putty Squad (which is basically the Killer App for the Amiga, even if it came out way too late). I could talk about these games the whole day. Also all those amazing Pinball games bring back so many memories as well, I sometimes still play Slamtilt. Slamtilt really was incredible, look that game up if you find the time. Its also amongst the highest rated game ever on the Amiga. I would love to see that game on GOG.

In another note, people who had Amigas (or still have them) praise Superfrog a whole lot but its not that amazing, though its still great, and it was on GOG as well. Too bad that GOG can't sell it again on here, due to legalities between Team 17 and another trademark holder who owns the name Superfrog. And to be honest, theres so many good games other than Superfrog that its not easy to not find good games on that platform :P!

EDIT: Edited some stuffs for slightly better readability and also fixed some grammar errors.

The Amiga version of Dragon Wars

Reading your last paragraph, I never realised that Superfrog had been removed from the store. I own it but will probably never play it here as I agree with you, it is not as great as some people say.
Some of my favourite Amiga platformers are Rainbow Islands, James Pond 2, Ruff n Tumble, Rodland and Flood.

I wish GOG themselves would be asking us these questions on which old games we'd love to see here.

Dude, Rodland was incredible and I loved Rainbow Island. From what I've heard the Amiga version of Rainbow Island is as good as the arcade original. I do still remember the Amiga music of that game. I also liked Ruff n Tumble but its a difficult game, incredible tech behind the game, though.

I also played the NES version but the music on that version gave me the creeps back in the days.

I would argue that almost all gameplay differences are either down to subjective taste or are a matter of flaws that one can live with provided that the game as a whole is interesting to the player - few such flaws would qualify as truly game-ruining to be discarded out of hand. Evaluating/quantifying gameplay is a much more complicated and subjective matter than evaluating/quantifying graphics and sound so it wouldn't make much sense for GOG to micromanage the selection between the PC versus Amiga/Atari ST versions based on something as subjective as gameplay. It's much more sensible to simply include both game versions across the board and let the users decide for themselves (with the help of relevant user reviews etc). which combination of gameplay and eye candy is the best fit for their particular needs.

In the case of Bard's Tale 3, the flaws really are that bad. Some of the most game ruining ones (based off the DOS version, which I believe is similar bug-wise to the Amiga version):
* Harmonic Gems are rare in this version, meaning that you will need to wait outside for long periods of time to recover your SP. (There's no Roscoe's, and SP regen is much slower than in the remaster.)
* Monster special attacks don't work. Monster physical attacks will never cause status ailments, while monsters that are supposed to have breath weapons will fail to use them; this bug affects both enemies and monster party members (so what's the point of a Dragon or Slayer?). (It's also worth noting that weapons like the Stoneblade are also broken by this bug, but that bug, while annoying, isn't quite as game-ruining.)

Edit: In other words, your qualification "almost all", I think, actually excludes these particular flaws. (With that said, too many Harmonic Gems could also be an issue (and is in some versions), but isn't as bad an issue as too few.)