The sad thing is there is no definitive version for SMB3, unfortunately.
All Stars
+Better Sound quality
-No ability to replay levels
-Physics are a bit off (too much inertia)
GBA:
+Ability to replay levels
+Physics are much better than in All Stars and closer to the original NES version
-Sound quality is SHITE
-Voice effects in the game
As for YI, I haven't tried the GBA version, but you can expect like with most GBA games, the sound quality will also be shite, however it's supposed to have extra levels or something. Still, yoo can't go wrong with the SNES one.