The train takes about 5 hours, but costs about €50-€55 one way. Might get a better deal depending on when you book. try www.bahn.de
as they might have deals on. i did see it as cheap as €29
Theres also a direct coach with eurolines
, but that takes around 6 hours and i think its a similar price too, or maybe a bit cheaper.
no idea about flying, but i think Berlin schönefeld (SXF) is the main airport for the low cost airlines
an alternative to hitchhiking is a couple of websites where people advertise spaces in their cars for long journeys for a fee. thats what i am using to get to Berlin at the weekend, and its costing less than half what the train would cost. www.mfz.de
is useful, but you cant see all the details unless you register. its all in German though too. i did just have a quick look and a couple of people are advertising journeys from berlin to prague, for as little as €15.