It's really weird that we got the Game Boy Color, then Game Boy Advance, then Nintendo DS when the GBC hadn't been on the market for long before the GBA, and the GBA hadn't been on the market for long before the DS, but we still got a bunch of GBC and GBA games despite that. Some neat games I really like that haven't been mentioned are the original
WarioWare and
Hamtaro: Ham-Ham Heartbreak. I like the experimental new stuff Nintendo tried with the GBA, like multiplayer where only one person needs a cartridge, the e-Reader, and GameCube+GBA communication.
Something a lot of people might not know is that the crunchy audio that's associated with the GBA is largely due to low quality samples and a low quality audio mixer that Nintendo supplied to licensed devs (there is no hardware support for playing multiple samples at different pitches like the SNES had; games did that in software), and homebrew games can sound a lot cleaner with better samples and newer audio drivers like
maxmod.
On the topic of homebrew games,
Goodboy Galaxy is worth a mention for sure; I haven't gotten around to playing a ton of it yet but it seems very ambitious and polished and I love its aesthetic.