FF3 has a game crippling bug in the steam port, so if you're looking at FF games on Steam, I'd avoid that one. (Some people have claimed to not have any issues, while others have had their progress halted from important items not spawning, as well as save files just vanishing for no reason)
I haven't heard any issues with the FFIV port. I'm actually really interested in IV myself and want to play it sometime soon, but it will probably be the PSP version that has interlude and after stories. I also prefer the 2D look over 3D models and voice-acting.