(*) The Super Famicon port of the game removed all three subquests and added in a Ghost Town where you saw people killed in the war. There wasn't very much to do in it besides see Karshwarl's dad and get his best axe in the game.
(*) The PC-Engine game threw out over half the game's soundtrack, remixed a few songs, and added three new ones. The Super Famicon port trimmed things down even more and played everything through SPC700 synth (making it lower quality audio than the X68000 version by far).

Other Changes:

The MSX, PC-88, and X68000 editions all have a large graphical intro showing (depending on the games) paintings or anime-style graphics depicting how Tamryn came to end up in Dragulia and when she left to go back to Ishuban. In most games, especially the X68000 one, it gives you a much better idea of what Atrushan and Tamryn's time together was like. The PC-Engine CD and Super Famicon ports completely omit this aspect of the game.

The PC-Engine and Super Famicon ports omit FIVE movements of the Opening song of Emerald Dragon. Only "Main Theme" is kept. "Prelude", "Cataclysm", "Reminiscence 1", "Reminiscence 2", and "The Immortal" are totally removed. "The Immortal" is recycled in a remix later in the PC-Engine title.

The PC-Engine and Super Famicon ports remove all three of the battle themes to replace it with one battle theme and one boss battle theme. All the shop themes are also removed and replaced with one universal shop theme. The multiple town themes are removed and replaced with one universal town theme.

The PC-Engine game removes the ending song used in the MSX, PC-88, and X68000 ports and replaces it with a medley of the main themes of the game. It's not a bad medley at all, I rather liked it. I do wish they had kept "Ending" though; it's a very gentle and sweet melody that really fits the way the game ends much better than the fast-paced medley.

The Super Famicon port added dozens of treasure chests to all the dungeons in the game making it incredibly easy to obtain powerful weapons without having to spend any money.

The Super Famcion port removed all realism from the game by adding a bottomless inventory. Previously your characters could only carry 6 items that they were not currently wearing (I need to double check the number, it may have been 8). On top of that there was no item counter so every Waramuru Medicine you had was one less slot. This often resulted in sacrificing items later in the game to pick up anything in dungeons.

All ports have different character portraits excluding the Super Famicon and PC-Engine CD ports. They share the same portraits, however, the Super Famicon ones look incredibly washed out.

The Priestess of the Ocean just gives Tamryn the Teleposta in the Super Famicon port. Previously acquiring the Teleposta was it's own quest in a cave.

Maps were redrawn in the PC-Engine CD and Super Famicon ports. In the PC-Engine CD some netting was removed from dungeons due to the machine's inability to handle transparency effects well. In the Super Famicon port, all dungeons were made much shorter and simpler and given much more treasure to acquire inside.

On average, at the end of the game you have roughly 380HP-490HP for every character in the MSX, PC-88, X68000, and PC-Engine CD ports. In the Super Famicon port, you will hit that in 20 minutes. It's not hard to be pushing 6000HP when you finish the Super Famicon game. The enemies were poorly adjusted to compensate for this, most bosses are far easier than they were before.

The Super Famicon game added Dragon Change attacks for Atrushan. You obtain a new attack for every Emerald Grace collected in the game. Most let you attack all onscreen enemies at the cost of a fraction of your life. Nothing at all was adjusted to account for this kind of damage. Boss fights that used to be incredibly challenging due to how many minions they had to poke at you are now a cakewalk to beat. This plagues the game from start to end.

The Super Famicon port added a map underlay to the "Party Converse" screen. This is likely because unlike the other ports, it did not come with a gigantic fold-out map.

The Super Famicon port lacks the incredibly bloody, violent death scene of Bagin.

The Super Famicon port adds an altar which basically screams "HEY STAND HERE TO GET ATTACKED BY RA!". Previously finding your way into Hellmand Mountain required walking all over until you happened to find Ra.

The Super Famicon port replaces the traditional bow and arrow character matching game with a different challenges in each casino. You can only win the prize once and first will be some kind of "Bunny" gear (from the Bunny Girl running the game). This equipment is incredibly powerful and was never in the game before (yet again making this version remarkably easy)

The Super Famicon port adds a series of bloopers/outtakes to the credits if you beat all the casino events.

In the Super Famicon port you meet Saoshyant before Yaman gets killed. In the other ports, Saoshyant shows up at the grave as you bury Yaman. My only gripe with how the SFAM port handles it is introducing a new archer type character and killing the old one seems like a massive story cop-out. The fact that Yaman dies so needlessly doesn't help (tries to push Atorshan out of the way of a sniper in the bushes and is killed by, yes, a bow and arrow, right after he was giving bow & arrow lessons to a little kid in the town. Oh the irony of cheaply written scripts)