I don't have a big collection but here are a few of my favourite hidden gems / underrated games so far:
Maniac Racers Advance (aka Motorcross Maniacs Advance) is a fun but overlooked title. Gameplay wise, it's a bit like Excite Bike meets Sonic the Hedgehog. Very fast and takes a little while to get to grips with.
There's Alien Hominid, which is an expanded version of the old Newgrounds Flash game. That's worth a look if you like Metal Slug style run and gun games. A bit short, but has smooth looking animation with loads of charm.
Columns Crown is a decent puzzler but not well regarded. It's just Columns tbh, so if you don't like Columns you won't enjoy it, but I like it.
V-rally 3 is a game that's lost much of its magic these days, but I still think it's very impressive to see a fully 3D rally car game running on the humble GBA. It even has a first person mode for added immersiveness!
And finally, there's Advance Guardian Heroes: A technically impressive and ambitious beat 'em up that doesn't quite hit the mark. But still, it's cool to see what the GBA can do when it's made to sweat. Treasure also made Astro Boy: Omega Factor and Gunstar Super Heroes (both are excellent).
Solid ports like Jet Set Radio, Super Monkey Ball Jr, Street Fighter Alpha 3 and Super Street Fighter II Turbo Revival are worthy of a mention too, but not exactly obscure.