There are a few things to consider when flying round europe.
They mainly are flexibility and timing.
A lot of the really cheap flights are early in the morning or late at night, it can be hard getting transport to/from early/late flights. As I am writing I am waiting for the london underground to start running as my flight came in a half hour after they stopped running. also have had to sleep on airport benchs so as to be able to make 5am flights because most trains don't start until 5.30am.
But it is definately the cheapest way to travel around a lot of europe in a short time if you organise it correctly.
Also the pricing fluctuates all the time, I booked a flight and then looked back at it literarly 2 hours later and the price had dropped by 10EURO. I was a bit bummed about that.
This is all with easyjet, which actually takes you to reasonably close airports to the cities.