Ok, I have done some research myself (thx for reminding me about hardcoregaming btw) and was able to answer my own questiion only partially. Regarding the original part 1&2 this game has been ported to probably every single platform conceivable, which considering the number of platforms throughout the years, means quite a lot of them. The problem is that each consecutive version is less of a straight port and more of a remake/remaster making use of better hardware. Because of this approach visuals and audio are not the only elements changed. There are more or less subtle differences in things like level layout, amount of grinding and combat difficulty. And I doubt you can understand them fully without experiencing all the versions first hand, which is out of the question for me.
Bottom line - the version offered here on GOG seems the ultimate version you can get (correct me if I am wrong), mayby with the exception of music soundtrack (with like a million different versions throughout).
Well I thinkt he remastered version on gog.com for Ys 1&2 basically put together the best out of the first Windows Port and one of the earlier original releases.
Basically what we have on gog.com right now is Ys 1, Ys 2 and Ys 3 (that is the oath of felghana, which is a new imaging of the original Ys 3) and origin which plays before the events of Ys 1.