I recently set up a Game Boy Advance emulator gaming station on an old laptop with a monitor and an Xbox 360 controller. I have used Visual Boy Advance emulator in the past, but after some research ended up choosing mGBA. The mGBA seemed to work best on an old low-spec netbook.
These are some fun GBA games to play on emulator with a controller.
Duel Masters: Sempai Legends
There are 3 internationally released Duel Masters games for GBA: Sempai Legends (2004), Kaijudo Showdown (2004), and Shadow of the Code (2005). Sempai Legends has the narrowest card pool, and this makes it the simplest one to play.
Very good duel gameplay
Graphics are not the best
The story and characters are not very good
Only 180 cards (DM-01 and 60 spells from DM-02)
Limited card pool makes the game more casual
Later GBA Duel Masters games have same the gameplay with larger card pool:
Kaijudo Showdown, 300 cards (DM-01 - DM-04)
Shadow of the Code, 600 cards (DM-01 - DM-08)
Super Street Fighter II Turbo - Revival
Works nicely with Xbox 360 controller, or any simple controller
Classic SF combat
Pokémon Emerald
Best of the 3rd gen Pokemon games
Very good music
The last true 2d Pokemon game
Castlevania: Aria of Sorrow
Perhaps the best GBA Castlevania
Works nicely with controller
Pokémon Pinball: Ruby & Sapphire
Quite casual pinball game
Fun bonus and boss levels
Nice Pokemon music
More GBA games
GBA has tons of fun games, here are a few more to consider:
The Legend of Zelda: A Link to the Past and Four Swords