NES.emu is the best NES emulator for Ouya. You shouldn't have any issues with it running any game that's part of goodNES.
As of the current version, there is controller lag if you use the stock Ouya controller with it. It's not the Ouya's fault - its a failing of the emulator. I have emailed the author and he assures me that this will be fixed in the next revision. For now though, you can use pretty much ANY other controller and it should function correctly.