CNN has an article that asks whether or not you should payoff your debt or keep your emergency fund. The answer, to me, is very simple. Always keep your emergency fund fully funded.
Our emergency fund is fully funded, and we definitely feel that it should be used only for emergencies. You should make sure that you are financially prepared in the event of any downturns in your financial propects. If you take your emergency fund and payoff your debt with it, you may find yourself in more debt later down the line with no buffer.