I am just wondering what the best version of Ys 3 is, and am also curious to know what little differences exist between the different versions. In particular, I am curious if there are any mechanical differences, or if there are bugs that are present in some versions but not others.

One other thing: I prefer NES-style 8-bit music to the music found in supposedly more advanced versions of Falcom works.

Also, before anyone mentions it, I consider Oath in Felghana to be an entirely different game, and I consider said game to be outside the scope of the topic. I am, in particular, asking for what the best version of the *original* Ys III: Wanderers of Ys is, so please don't suggest OiF (which I have played and enjoyed, by the way, but it really isn't the same game).

I haven't played every version of Wanderers from Ys, but I'm assuming the PC-88, X68000, MSX, and Famicom versions are not on the table anyway. There's also a Japan only PS2 port I'm not familiar with.

However the three main versions, the PC Engine/TG-16, MD/Genesis, and SNES versions I can shed some light on. All 3 of these versions have major differences including game balance. Going from memory here, but I believe the TG16 version is a little on the easy side, the SNES version is quite difficult, and the Genesis version is kind of in the middle.

The TG16 version has arguably the best soundtrack in the entire series. I'm not a fan of the remixes in Oath/Origins either, but I really like the arranged soundtracks of Ys 1-4 on the PC Engine/TG16. However despite the fact that Ys 1&2 got an excellent English dub on the TG16, Ys 3 has a horrendous English dub. Also the TG16 only has 1 background layer, but the game still tries to do some parallax scrolling and it is really jerky and distracting - to be fair, the PC-88 original has this issue too. Overall this is a good version.

A lot of people will dispute this, but all Ys games on the SNES are terrible, don't play Ys on this platform. The SNES' sample based audio chip is completely incapable of reproducing Falcom's synth based music. This version also does not take advantage of the graphical capabilities of the SNES at all. There's no reason to play this version, although you could probably get the original cart for a tenner.

The Genesis version is actually my favorite. It has proper parallax scrolling, and I like the difficulty balancing best, as I mentioned earlier it's a little more balanced. Its soundtrack is also very faithful to the PC-88 original, and in my opinion it even sounds better than the X68000 version.

Short version: for best gameplay/visuals play it on the Genesis, for best music play it on TG16, PC-88 emulator, or again the Genesis

Trivial answer but what do you mean under "best"? Oath of Felghana considered to be the canon by Falcom thus it has the best connection to the series. Gameplay-wise it is really up to you. Ys III hold the position of the worst Falcom game based on the critics. (or at least Falcom based game as the PC-Engine and other ports aren't developed by Falcom but this is the same with Ys I & II when it comes to console vs remake, the PC-88 and 98 as well the newer remakes are the only Falcom developed games).

As I said in the OP, I consider Oath in Felghana to be a different game, and noy a version of Ys 3: Wanderers of Ys. Hence, it is not under consideration for purposes of this topic.

Then play the PC-88 or PC-98, that is the closest you get that still canon more or less though after Oath of Felghana Falcom made that game to be a spin-off.

I am not actually concerned about whether the game is canon or not; I am only concerned about which version is best as a game.

Also, I am interested to know what the little differences between the different versions are. For example, I've heard that the SNES version, which is the one I played when it came ount, is harder requires more time spent farming experience than, say the Sega Genesis version (not to mention that the Genesis version has a bug that allows you to get maximum level and gold early). So, how do other versions compare?

In particular, you mention the PC-88 and PC-98 versions; how do those versions compare to each other?

Also looking at other versions like the MSX and NES versions: How are those two?

The PC-88 and 98 are sidescrolling, the two are identical but the 98 has better resolution and higher sound frequency so that is preferable. I never played the Famicom, Super Famicom and Megadrive version, I can't say anything about those. If I remember right the Super Famicom also sidescrolling considering the old commercial video. The PC-Engine version is a spin-off compared to the original 88 and 98 as it alters the story at some point and it was not developed by Falcom as I said. And while you not asked that but Oath of Felghana also identical to the PC-98 version storywise but it extends a lot of scenes that wasn't in the original release due to the low capacity of the old computers and consoles.

Honestly I'm more interested in the continuity than in the gameplay because the Ys titles are way too easy except for the PC remakes. However this really ends at Ys I, II and Origin as the other titles barelly can be called Ys at all. Ys VIII comes closest to the atmosphere of Ys I and II and I wouldn't wonder if Falcom will make connection between Reah, Feena and Dana in the upcomming games. I don't really want to support game making that has no connection with the original concept so I just bought the computer remakes.