My Ouya decided it didn't want to pair the original controller any more, so I performed a factory reset after backing up all my apps with TitaniumBackup. Then I performed a factory reset, which doesn't. It left a couple of apps behind, including ES task explorer. Upon entering the adb shell, I found I could no longer su. The fix in my case was to reinstall superuser.
drink@alexander:~/Downloads/ouya superuser$ sudo adb shell
shell@android:/ $ su
1|shell@android:/ $ which su
shell@android:/ $ ls -l /system/bin/su
lrwxrwxrwx root root 2013-06-25 21:05 su -> /system/xbin/su
shell@android:/ $ cd /system/xbin
shell@android:/system/xbin $ ls -l su
-rwsr-sr-x root root 366952 2013-06-25 21:05 su
I don't even, either. But reinstalling the superuser and busybox apks worked without incident and now I can su again.