There were more versions of FFIV by the GBA port then there are of FFIII now.
DS (crappy remake)
PSP (port of crappy remake)
Kindle (port of the port of the crappy remake)
Super Famicom (original)
SuperNES USA (easytype)
PSX (Final Fantasy Chronicles port of original)
Wonderswan Color (buggy and condensed port of the original)
GBA (port of the WSC port)
And that's not including the versions that came afterwards like the DS remake or the PSP collection or any of the VCs/PSStores versions.
Lunar. Lunar has been ported waaay more than CT. GAME OVER MAN, GAME OVER.
Seriously though, CT is awesome. Glad the android gang can get in on it.
PSX (Final Fantasy Chronicles)
DS (first to include bonus dungeons)
Wii VC (of the original)
PSOne Classics (of the FFC emulation)
PSX (Silver Star Story Complete)
GBA (Legend sudo-remake)
PSP (Harmony of Silver Star)
iPhone/Pad/Piece of whatever (current)
Although if you don't count the various VCs and PSStores then yes, Lunar holds more remakes by one iteration.