The Dolphin Team have released a new version
of the Gamecube and Wii Emulator for Windows, heres whats new

Changelog for r7121

Change to the 1.3 part of the Xrandr api for fullscreen mode switching on linux to support multiple monitor setups. There is probably some more work to be done, but at least it won't shut off one of your monitors anymore

Download Here --> http://www.dolphin-emulator.com/download.html