The Wind Waker has tuner runs, which require a gameboy something or other (the handheld Ninty console around 2002) and a connection cable to link it to the Gamecube. In addition, Twilight Princess HD 100% runs are of two forms, the first which bans all Amiibo and the second which allows all Amiibo (and requires the Wolf Link Amiibo). There's others out there, these are just two I can think of off the top of my head at 4am.
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