the myriad of JRPGs I could suggest aside... (There's a little guy out there that only came out for the Super Famicom developed by Square that I want to suggest called Treasures of the Rudras that has ZERO chance of ever seeing the light of day outside of japan in the history of ever thanks to the fact that the fan translation basically had to rebuild the game from the ground up due to the game's very innovative spell system.)
actually... I kinda would like to Nominate Treasures of the Rudras if you folks are willing to herd the forum into rounding up emulators like you did for Mother 3.
But, if that's not on the table, I nominate Startropics or it's very estranged sequel, Zoda's Revenge: Startropics II.
or, if we're going to rock the GBA theme that TYP is suggesting, I suppose I wouldn't mind going with Advance Wars: Black Hole Rising or Castlevania: Aria of Sorrow.