While Lufthansa doesn't usually have the cheapest fares, it's probably the best value for money and the best time of day in Europe. Tickets to virtually all destinations in Europe can be found between 147 eur and 257 eur, and it flies to most places several times a day, which gives a lot of security in the event of flight delays (you'll be on the next flight).
Outside of Europe, Lufthansa is usually one of the most expensive options.
From Prague, it flies several times a day to Frankfurt and Munich.