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
Nothing crazy much to add but the Kingdom Hearts game was really good, one of my favorite from the series.
Seriously? No Mother 3? No F-Zero games with three to choose from? No Boktai? And Summon Night Swordcraft Story didn’t make it either.
Plus, three Sonic Advance games, multiple Metroid and Zelda titles, but couldn’t spare a slot for Mega Man Battle Network anywhere?
At least it wasn’t full of Pokémon. Reads like a top 40 radio station set list, but for gaming.
Max Payne’s gba port was really impressive. Check it out if you haven’t already :)
Super Mario Advance 1,2,3 and 4
Warioland 4 is amazing, and definitely one of Nintendo’s greatest achievement. I didn’t appreciate the weirdness as much as a kid, but going back to it, I simply love how off the wall it goes, and how it is halfway a Mario platformer and halfway a sonic game due to you having to rush back through the stages. If you have ever played Pizza Tower, this is the game that inspired it.
Speaking a Wario, the Warioware games were some of my favorite pick up and play titles. There is just so much to do, even after you finish the short campaign. The DS one is by far the best one though.
Dragon Ball Z Legacy of Goku 2 and Buu’s Fury are some of the best Dragon Ball games period, and are pretty decent RPGs in their own right as well. I more or less experienced the entire story of Dragonball Z through those games, and they do a fairly decent job of retelling the events (Aside from the first Legacy of Goku game, which is garbage.) If nothing else, give the music a listen. Not only are their some good remixes of the American DBZ soundtrack, but a lot of original songs that are masterpieces.
I may add more if I think of any
I’m surprised at the lack of Drill Dozer. Seriously, give it a try.
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
Mother 3
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