I have to say Minish cap from Legend of Zelda for Game Boy Advance. The swords are awesome, the weapons are awesome, and the storyline is awesome. (Though the plot isn't that awesome...) I also loved Bowser's Inside Story for DS. The bosses were REALLY *****KING HARD but the equipment was great, and I loved the gameplay.
Last but not least, I'd have to say Pokemon Emerald for GBA, which was probably the best game ever for GBA. I researched for long, hard, cruel days. It really had some of the best Pokemon and legendaries, but it restarted on me twice (bad egg ebay seller!). I never did really beat the whole game...