The biggest album with variations is Then Play On. (I'd almost kill for an original.) They really need to revamp the CD and make it a two disc set: Disc 1 would have the original album, while Disc Two would have Oh Well, the unreleased Jeremy EP, and maybe Manalish and World In Harmony.
The first US pressing of the debut album had a pink border.
Bare Trees also had a very slight variation, with some covers having a small border.