FF4, my thoughts over here. I agree the 3D remake is a different game.
FF5, best version: SFC. Best English, official version: by default, GBA. The PS1 version has an amusingly bad translation that’s never been reused where Faris talks in POIRATE SPEAK, ARR. This isn’t discussed much, but it’s quite buggy: did you know it’s one of the only games to show major errors in Sony’s official internal emulator? It’s definitely not ideal to play it on PS3.
FF6, gosh. Again, I’d just as soon prefer the SFC, but in English I don’t think the original translation was anything special, and the GBA update preserves all the meme quotes anyway.
This goes for all the WSC / GBA ports: the colors are washed out and the music is tinny, there are fan patches that correct these problems if you can do that. The new post-game content they add is pretty fun, actually.