Yoshi's Island, for one reason: they replaced some of the sound effects especially the DAMN ANNOYING groaning sound effect Nintendo created for Yoshi's Story and thinks it's so brilliant they need to reuse it ever since. It's easily as annoying as Mario's whining.
(oh, and I don't think the levels were designed to compensate for the lower resolution, I'm looking at you 1-Extra, you were out-of-place difficult on the SNES and even more on GBA. Did the SNES version also makes enemies active before they even appear on the screen, I can't remember? The one Red Coin Shy Guy in 3-Extra made me want to nearly chuck my 3DS across the room.)
Of course Nintendo release this game again, it'll be this Special Edition because it requires less work than emulating the Super FX (and assuming the descendants of Argonaut don't have legal claims on the SFX).
FF6A would be a good port if the sound quality wasn't poor and it didn't have slowdown (especially the Rising Phoenix blitz, I think it was called.)