I would have to reinstall and verify, but I believe "lightflow" had that option. (disclaimer, I had the pro version in ICS, did not reinstall it after the JB update.
I have Light Flow Lite. You can set the percentage and a color/notification for each state so I have low battery set to blink red at 10% (extended battery), steady red when charging, and it set to change to steady green when it reaches 90%.