The transmission. There was slippage and when taken to the dealership they couldn't identify the problem. We took it to a transmission shop and it was a $3,000 repair.
Although we haven't had any problems with the car until now, a $3,000 repair is not something you want to hear. When looking on the Internet I realized I wasn't alone. It appears Ford Escape transmissions fail. Plain and simple. Maybe someone from Ford can tell me why I shouldn't consider a Honda next time.
Did you change the trans fluid regularly? If not, no automatic trans will last much past 80-90K.