@grizzlywhisker @FeelsOttoMan @LittleTom >Idk if there were any others besides Zelda Four Swords
Wind Waker had the Tingle Tuner, which was essentially a glorified cheat code engine, if you had enough rubees for the various cheats. All the Pokémon stuff on the Gamecube could interact with all the Pokémon stuff on the GBA. Animal Crossing was one of the rare games that had interaction with the e-Reader system and had multiple uses for the GC-GBA link. If you had Metroid Prime and Fusion, you could play the original Metroid. Sonic Adventure & 2 Battle allowed you to transfer Chao to the Chao gardens in Sonic Advance 1 & 2.
Those are the big ones I can think of. Unfortunately, many of the other games that used the link used it as a glorified minimap or a proto-DLC dispenser instead of something more cool like what Nintendo and Sega did. By the time you get to the late stage of the Gamecube's life, it seemed like everyone and Nintendo abandoned it.
t. Gamecube-fan