The VC download is the original n64 title, it's turn based. The one on gamecube is also turn based as well, and won't come out on VC as you can just pop the cube disc in and play. The new one on Wii, Super Paper Mario is not turn based.
All of them are fun, and different from each other. Just realize that the graphics are limited on the VC download, and it's hard to look at it after playing the other versions where they have significantly cleaned them up graphically.