It was driving me kind of crazy that there were no file manager apps available in the OUYA store. Sideloading is easy... if you can manage to sideload Dropbox or a file manager app first. So I went ahead and published one myself. It has a "touchless" interface that was designed specifically for use with gamepads.
Right now you can find it in the Sandbox section. Or just search by name (FilePwn). If you like it, please give it a thumbs up to help it out of the sandbox. A description of the app can also be found on this page
BTW I added some subliminal advertising for Mupen64PlusAE in the screenshots