Chrono Trigger
Ico/Shadow of the Colossus (original and PS3 version =P)
Super Mario Bros for the NES
Super Mario World (SNES and GBA)
Metal Gear Solid 3 (Original and Substinance)
Ninja Gaiden (XBox and Sigma)
Ninja Gaiden II (NES and SNES Trilogy)
Metal Gear (NES and MGS3 Substinance)
FFVII (PSX and PC versions)

There are probably some others lurking about but they are not coming to mind. I have also bought the same game multiple times because I lost a copy and this mainly relates to old as trout PC games that I got as a part of some pack on steam.