I have all 3 versions, all are totally worth playing.
MSX one is still quite awesome. It's also the darkest and goriest. If you play it on a Turbo-R and use the special boot disk, it plays silky smooth too.
X68000 is a remake of MSX, but it's still a very different game, longer, fantastic graphics and music. Due to the class change system, the game strategy is a bit different, but fuck it's still insanely hard.
MD, this is a total remake by PAL Soft, overall this is the most balanced for sure, it's all designed around just one character, and the random luck based parts have been removed. Plus you don't have memorize the minefields of hidden chests from the previous versions. In other words, it's a pure skill game now.
