That's a good question. There's probably at least two dozen games I bought three times with remakes/rereleases or VC, but more than that, I don't know. I keep everything, so there's no much need to do this. Maybe some unlockables games like Metroid, indeed.
The only game that made me triple-dip with only localization differences is Sakura Taisen V (bought the original JP version when it was published, the PS2 US version for the dual japanese/english, then the Wii EU version, which was mostly a way to show support)