I guess I better chime in, as I profess to being a fan of the color-screen beast from the 90's.
Dragon Crystal- a rogue-like that was on the Master system, but had better music on GG and is better suited to a handheld anyways (despite the smaller screen area) (also on the Nintendo 3DS store I think)
Baku Baku- Very underrated puzzle game in the same vein as Puyo and Puzzle Fighter; was on the Saturn, but again, well suited to a portable.
Crystal Warriors- has been mentioned, but really is a great little strategy/tactics game
Fantasy Zone-different than the original; not sure if hidden gem or a top game, but overlooked IMO
I 2nd Devilish as a good pick for hidden gem.
Let's see, I really like the Space Invaders game (port of '91?)
Really, I need to dive back into the catalog. There are so many I still need to play just in my collection.