The long times are incredibly long on the MSX version.
The "Team Metalslave" logo is missing on the MSX version.
Some, if not all of the sound effects are different.The sound effect on the MSX version, whenever a shocking discovery made, is extremely loud, it scared the fucking shit out of me, the first time I played it. Make sure to have your speakers down most of the time.
The PC-88 version allows you to turn off the bleeps and boops when someone is talking by pushing the CAPS lock. This does not happen in the MSX version.
The PC-88 version came in 5 disks. One was the main one for disk drive 1, and the other four, were for disk drive 2, which would be different depending on the location in the game. The MSX version came in just three disks and a Sound Cartridge.
Some of the tracks exclusive to the MSX version, do not appear in any of the other versions.
In the PC-88 version, in the scene where Gillian and Metal discover the damaged Little John, there was a wide shot of Metal standing there, about to retrieve its "memory", just before we see a close-up of it. It was cut in all the other versions.