Off the top of my head:
SaGa 2, the remake of the second SaGa game for gameboy that you might know as The Final Fantasy Legend 2. There's a translation patch by crimson nocturne.
Space Invaders Extreme 2. I'm not quite sure how it went under the radar.
Legend of Zelda Spirit Tracks. I'm only listing this because I know a lot of people passed it over after being disappointed with Phantom Hourglass, but they vastly improved on the gameplay and it's very worth playing.
Drone Tactics, a very good strategy game. Can be a bit easy sometimes. For those skeptical, it involves bugs with laser cannons.
Rondo of Swords, another commonly overlooked strategy game. I haven't played it much, but it has pretty fluid gameplay.
I've got a large list of these somewhere.