There are two official taxi companies at the Prague airport. They have a frontdesk at arrivals in both terminals and you can find the taxi waiting area in front of both arrival halls.
If you want to be sure about the price in advance it is better to call a central dispatcher instead of taking taxi from the airport. There are many companies that are specializing in airport transfers. They don't have a problem checking you flight status and adjusting to it. They don't have charges for a waiting time and there is no drop charge. If you are going to the downtown of Prague it will cost you around 500 CZK.
Some of these companies:
Transfer Praha: www.transferpraha.cz
Prague Transport: www.praguetransport.com
These companies are a good alternative to the taxi services. They are very comfortable. You pay prices set in advance which can sometimes be better then taximeters.
If you are staying at a hotel in Prague, the hotel will provide you with a number or arrange a taxi for you. The rate of hotel taxis are in general higher than pre-ordered transportation. Higher price is compensated by better vehicles and guarantee that it is safe.
Unfortunatelly taxis in Prague are known for their bad reputation. There is a group of companies in the city center that will try to rip you off. Things are getting better now and authorities are trying to make all taxis act fair. Maximum taxi rates by the law are – drop charge is 40CZK plus 28 CZK per kilometer and 6CZK per minute of waiting time. If you are travelling between the downtown of Prague and the Prague airport it will cost you around 500-700 CZK. Taxi rates from dispatcher should be cheaper. Around 20 CZK per kilometr and it is definately more safe than a taxi from the street. You can usually pay in Euros as well. Here are some taxi companies :
City Taxi: www.citytaxi.cz/en
Modry andel: www.modryandel.cz/en
Tick Tack taxi: www.ticktack.cz/en
If you are looking for very comfortable and quick way of traveling from and to the airport and you don't mind paying little money then you should definately choose some of these services. If you are looking for cheaper options you can use public transportation which is the cheapest way.