I want to start collecting these, but I can't find a complete list of them all.

Here is the list I have now. As people contribute I'll update it:
4-Player Extra
Advance Wars Dual Strike
Batallion Wars
Donkey Kong Country
Final Fantasy
Final Fantasy IV Advance
Jet Force Gemini
Luigi’s Mansion
Mario Kart 64
Metroid fusion
Metroid Prime
Metroid Prime Echos
Metroid Zero Mission
New Super Mario Bros.
Ninja Gaiden II
Pokemon Colosseum
Pokemon Crystal
Pokemon Emerald
Pokemon FireRed/LeafGreen
Pokemon Gold/Silver Pokedex
Pokemon Gold/Silver Walkthrough
Pokemon Red/Blue
Pokemon Red/Blue/Yellow
Pokemon Ruby/Sapphire
Pokemon Snap
Pokemon Stadium
Pokemon Stadium 2
Pokemon TCG: The Video Game
Pokemon XD: Gale of Darkness
Star Fox Adventures
Star Wars Rogue Squadron
Super Mario Advance
Super Mario Bros. 3
Zelda: A Link to the Past
Zelda: Majora’s Mask
Zelda: Orcarina of Time


I know there are a ton, and it'll be a tough collection to complete, but I love these guides.