Do you know offhand of any other variants (aside from Ys retail and Ys duo pack-in)?
That depends how deep you want to take it.
Theres the 2 Chamions Forever Boxing red and black variants. As well as a poster that came with some of them (I've only ever seen two of the posters).
Theres actually 3 versions of Ys. 1) Retail 2) Pack in version 1 that says Made in Japan on the disc and has a white case but no back insert. 3) Pack in version 2 that says Made in USA on the disc and has a black case as well as a back insert.
Theres two versions of the Hudsons Game Music CD. 1) Has a front insert 2) Has no front insert.
Insanity has a few versions. 1) CCAG version 2) Preorder version 3) regular release.
Meteor Blaster DX has a few also. 1) CDR first release 2) Signature Edition variant 3) Second printing on a pressed disc.
These are the one's I thought of quickly. If you want pics of any of them for reference you can see them on my photobucket link in my signature.
