Even with an EU unified currency, the local cost of living will play a large part in determining the market for salary. Other barriers to mobility (language, family needs, etc.) create partitions in the EU workforce that can lead to imbalances in salaries and cost of living.

Prague's prosperity may have caused the cost of living increases to outstrip salary increases. However, Prague may still be relatively less expensive than Berlin, Paris, or London where salaries may be commensurately higher. The key is to find the best ratio of salary to cost of living. In the US, one can work out decent estimates of this ratio using cost of living calculators. I don't know if similar measures are available in the EU.

Update: Here is an international salary calculator to get an indea of relative cost of living.