LogFAQs > #926193782

The DS has more depth in its library (and is probably better overall), but the GBA is definitely my personal favorite.

Obviously if you include BC the DS gets GBA games (and the GBA gets GB/C games, which isn't as good IMO), but that makes for a crap comparison. The DS has better hardware too of course.

So basically, the brain says DS but the heart says GBA.

Some of my top GBA games:

Metroid Fusion and Zero Mission
Mega Man Battle Network (mostly 2, 3 and 6) (Double Team DS is also cool)
Castlevania Circle of the Moon and Aria of Sorrow (the DS ones are arguably even better on average if you include HoD with the GBA ones)
Legacy of Goku II & Buu's Fury
Mega Man Zero 1-4 (think there's also a collection on the DS)
Super Robot Wars Original Generation 1/2 (also A/D/J/R for JP only games)
Advance Wars 1/2 (supposedly the DS ones are good)