Probably FFVI is the most. I have the SNES copy, the Anthologies versions, the FFVI Advanced for GBA, and I have the Super Famicom version as well as an emulation version.

FFIV - SNES versions, FFChronicles version, FFIV Advanced, and FFIV DS.

Persona 3, I have the original versions that came with the art book and soundtrack, the P3:FES, and Persona 3 Portable.

Chrono Trigger - SNES version, FFChronicles version, and DS port.

There are a few others I have multiple copies of but I'm not in the mood to list them if they are under three formats.