Is there a way to reset my settings?

[justice_network]

I want to do a semi clean version of Dolphin but I don't want to delete my saves or anything.

[JosJuice]

Go to the Dolphin Emulator folder in Documents. You can delete the Config folder in there to get rid of pretty much all the settings. GameCube save files are stored in the GameCube folder by default, and Wii save files are stored in the Wii folder by default, so deleting just the Config folder won't get rid of save files.