Renting a car is not always the best option because it is difficult to find companies that let you cross borders. If you do find one that allows this and lets you drop off the car in another country you will pay very steep fees for the service. Also there is a certain risk in driving a relatively new rented car around certain areas - non-local license plates can be a sign for "steal me". (There is a very good reason Germans do not like to travel by car to Poland.)
In addition train and bus travel are very cheap in Eastern Europe, so look carefully before you decide to go by rented car.
You can figure out costs for train travel by using www.jizdenka.cz
If you do decide to go by car get in contact with a used car dealer in Germany, Czech Republic or Poland who is exporting old used clunkers to Turkey, Russia or the Balkan states. Try to make a deal where you buy the car for say 500 EUR, but he installs the (export) licence plates and picks it up later, say in Istanbul. If you want to do that look into going to Berlin first before you hit Prague.
P.S: Could you pretty please fill out your profile? I like to know who I am talking to.
Plus everybody here can give more detailed advice if they know your age, interests, languages you speak, your citizenship, countries you have visited before, your travel plans (are you on an RTW?), whether you like to travel with a tent or not, what is your budget/comfort rate, etc. etc. etc..
[ Edit: Edited on Nov 7, 2008, at 6:55 AM by t_maia ]