LibHomebrew - Free60
Mupen64 (N64) worked with a couple of games I tired.
nulldc (Dreamcast) not tested by me
You can launch from FSD using Xell Launch with the EMU on a USB stick, one day we might get support for a libxenon boot selection so you can have all your libxenon programs on one stick and select on boot but for now easier to have one on each USB stick.
Haven't heard of anyone working on one for gamecube but no doubt gligli can do it question is only when....
Edit, full list here http://www.free60.org/List_of_homebrew_applications