I'd say the DS version of IV is better if you are looking for better gameplay options. The GBA offers two optional dungeons at the end game and the ability to switch out party members at the end as well. Course the difficulty took a hit to keep game balanced intact. The DS version sports a new skill system and greater difficulty levels. Its two optional bosses are not as fun as the the ones from the GBA but the revamped story bosses more than make up for it imho.

If you still want to be a traditionalist and plays something closer to the original, I say go for the PS1 version in FF Chronicles as it has a better translation than the SNES version but retains the original difficulty of the Japanese version.

I second Kishi's recommendation for the PS1 version of FFI and II cause its more true to the original games, the graphics are not as garish and the difficulty is still there.

I do recommend the GBA versions of V and VI if only because their translations are beautiful and offer greater appreciation for the stories. The Extras are neat but not really necessary. Gameplay is the same in all version except the GBA version of VI doesn't have the uber cheap Vanish/Doom trick anymore.

I cannot offer any advice for the PC games.