Browsing around (and by browsing around I mean going through the internet with a fine-tooth comb) I found some, if not hacks, game-altering codes for GC games.
http://www.romhacking.net/hacks/2859/ - SoA hack by Maeson, the guy is a hero
https://forums.dolphin-emu.org/Thread-skies-of-arcadia-hd-v0-05-november-13-2017 - SoA HD texture pack, unfinished but very nice
https://forums.dolphin-emu.org/Thread-ar-gecko-codes-for-paper-mario-the-thousand-year-door-ntsc-u - TTYD difficulty AR and Gecko codes - played a full game with one of these - x1.5 enemy and boss health was a nice change
https://projectpokemon.org/home/forums/topic/35897-first-pokemon-colosseum-randomisedhack/ - Colosseum randomizer
https://www.blastsoftstudios.com/downloads/smsmulti.html - Sunshine multiplayer, actually works fine, but is kinda janky
Hope this makes it easier to find some nice GC hacks, and I hope people post more hacks that they manage to unearth. It's still a relatively young modding community I understand, and a bit split up into separate camps.