Harry Potter and the Chamber of Secrets has an interesting and involved Gamecube-to-GBA link mode. In fact, it has two!
The first is a not-fun 9 tile slide puzzle that does not require a cartridge.
The second option unlocks content in both the GBA version and Gamecube version. You’ll basically need nearly complete save files for both games and it takes work, but players can access exclusive areas by linking both games a couple of times. Collectable in-game cards are the reward, even though they do not do anything.