Obviously it depends on where you come from as to whether or not you'd consider the market in Munich cheap.
Most, if not all, other places in the country are cheaper than Munich for used cars. Use the www.mobile.de
websites and you can locate various second-hand cars anywhere in the country. Then it just depends on the car and the price as to whether or not it's worth your while making a trip to buy it rather than paying a local price.
Even if you don't buy using these sites you can use it to gauge average costs for various motors in different parts of the country by entering post-codes and search radii.