The battery/motor has to be replaced just like a regular car battery. The average hybrid car with get about 109k miles on a battery before it needs replacement, though some Pruis owners have claimed 170k+ on theirs. I guess it depends on your driving habits. People who drive lightly and use the electric engine more will wear down the battery faster than the gas engine. Likewise if you accelerate hard and use the gas engine more. Nevertheless, the battery will need to be replaced, much sooner than a traditional petro-engine does. Its basically the hybrid equivalent to an engine swap. I've read on average they cost around $2,300, almost comparible to a petro-engine's swap. A powerful battery for a Lexus hybrid might be $3,000+.
Right now as it stands, diesel engines are rated at the most efficient overall, in terms of fuel economy and cost to the owner. Diesel fuel costs comparible to petro fuel and gets a much higher fuel efficiency. Just compare a gas Volkswagen Beetle to a diesel one. The gas one gets 23/32 mpg, while the diesel gets 35/42. Also, newer, cleaner diesel engines are coming out in Europe that are just as environmentally friendly as petro engines.
What worries me the most is that hybrid cars are going to scare away the consumer market from the movement towards alternative fuel. We had an environmentalist speaker come to our college several months ago, praising the hybrid car and telling everyone to buy it. People are going to buy hybrid cars an expecting Corolla efficiency and dependability, but its definately not. Studies have shown a hybrid car over its lifetime can cost as much as a light truck or SUV.