Excluding ports, my favourites are:

Final Fantasy Tactics Advance

Golden Sun series

Hamtaro: Ham-Ham Heartbreak

Hamtaro: Rainbow Rescue

Mega Man Battle Network series

Pokemon series

Sonic Advance series

Sword of Mana

Summon Night: Swordcraft Story series

Not mentioned here yet:

Metroid Fusion and Metroid Zero Mission

Mega Man Zero series

The Legend of Zelda The Minish Cap

Fire Emblem The Sacred Stones

I had tons of GBA games but the one I remember most fondly is Link’s Awakening DX.

Second would be uh… Damn, I forgot the name of it! It was that Hideo Kojima game with a solar panel in the cart because it used sunlight as a gimmick. It was the closest thing to a MGS game there was on GameBoy at the time, and I loved it. Didn’t care for the gimmick tho. You couldn’t actually see the screen if you were in direct sunlight which the sensor needed (unlike my damn calculator, using a lamp didn’t work).

Edit: Boktai! You mentioned it further down in the comments lol