Auto-rickshaws and taxis are a cheap, convenient option for getting around in all the big cities, and can also be hired for an entire day of sightseeing. Be prepared to bargain, though.
Fares for an auto-rickshaw ride, especially one in Agra, depend on several factors, including how wealthy you look, how far you want to go, how many times you want to stop, the time of day, and whether it's raining. You can generally expect to pay about Rs. 600 for a half day, Rs. 800 for a full day. If you're not comfortable with the price you're given, look for another auto-rickshaw, and if you don't want to haggle, take a metered taxi or book a car.
Auto-rickshaws are a fast way to scoot through crowded city streets, but the fumes from other automobiles can be horrendous at busy times. When traffic is heavy, take an air-conditioned taxi with the windows closed, especially if you're coming from one of the hotels far from the ghats. Ask your hotel or the tourist office for the going rate, and agree on a fare in advance.