SMS and TG-16/PCE version def are the best, but I think the TG version is too easy.
In the TG version, you can just move one screen away and the monsters will regenerate. This makes it really easy to collect EXP points and level up. But besides that point, it's my favorite series.
In the SMS version, you have to leave a section completely before monsters will re-gen (i.e. goto Minea then head out again), so it's harder to level up. I played the SMS version way back when I was 11 on my SMS. Fell in love with that game and got all the way near the end of the Darm Tower, but didn't know how to stop that level with the evil music playing. I somehow managed the un-managable - I got thru that level running thru the music, used some healing, and then got stuck. When I backtracked to that Luther Gemma level, I was stuck and died.
The NES version isn't too shabby. I like the tunes, and the controls.
Not as nice looking as SMS/TG though >_<