I've done some searching and I'm curious as to what these variations are really. The examples I'm using are for Zelda oracle of ages (pics found off ebay).
http://www.flickr.com/photos/49234216@N08/4589347007/
http://www.flickr.com/photos/49234216@N08/4589347073/
One you will notice has a flat bottom (Picture 1). This version doesn't have a removable tray insert but instead has it housed inside the box for the game. The second version (Picture 2) seems to have a interlaced bottom box and instead has a removable tray insert that you can pull out from the box, and it has a holder for the game.
Does anyone have more information on this? I don't know if one was an earlier printing, or what. But if so does this trend carry on for other Gameboy and gameboy+ games? Is there a list available if so? Excuse all my questions, I'm a very curious man.