Mine is Lady Sia for GBA. It's just a platformer but I just love it played and completed more 20 times. Will probably speedrun it in future.
If we're talking RPGs like a lot of people in this thread are, while the Zelda GBC/GBA games were great of course (although not so obscure), I also really enjoyed Golden Sun. I believe another game I also played when I was younger was Racing Gears Advance, I think that one was a bit more obscure.