I & II - PlayStation. Bug fixes, and better translations. Also, the GBA and PSP versions are so dumbed down that there is hardly even any challenge. NES versions are second best because of their difficulty, but they are filled with bugs.
III - Probably DS over the NES version. I hear it's more balanced, but I think both versions have serious flaws. I prefer the NES version to be honest, but I can see how the DS version is "better".
IV - The DS version is my favorite. But it's so different from the original 2D version. I'd say the best version of the 2D game may be the European GBA version (bug fixes over the NA version)
V - GBA version, no contest.
VI - GBA version. Slightly better translation and bug fixes.

Don't bother with the PSX versions of IV throught VI, the wait times are ridiculous and V's translation is probably the worst thing I've ever seen.