Prague-Berlin is about 45 EUR regular fare and Berlin-Amsterdam is about 120 EUR regular fare.
But if you book online in advance through www.bahn.de you can get special offers - 19/29 EUR for Prague-Berlin and 39/49/59/69/79 EUR for Berlin-Amsterdam.
Alternatively you can also use special discounted train tickets that allow you unlimited travel on regional trains (Laenderticket or happy-weekend-ticket). With this method it will be 37 EUR from Berlin to the Dutch border and about 30 EUR from the Dutch border to Amsterdam.
For Berlin-Amsterdam you can also look at budget flights and for Prague-Berlin at bus transport.
http://www.skyscanner.net
http://czech-transport.com/index.php?id=351
Recommended stops enroute:
Dresden, halfway between Prague and Berlin - leave Prague early in the morning, visit Dresden and continue later in the day to Berlin. Around Dresden the Koenigsstein Fortress is really worth seeing. To get there get off the EC train at Bad Schandau and take the S-Bahn (small local train) to Königstein.
Spreewald, a unique area of irrigation channels just south of Berlin. The "capital" of the area is Lübben. Both Lübben and the smaller Lübbenau can be reached by train from Berlin and from Dresden. Rent a bicycle or a canoe and explore the area that way.
http://en.wikipedia.org/wiki/Spreewald
spreewald map, pdf file
Quedlinburg - a great old city with a completely preserved medievial inner city. The place is about 3 hours away from Berlin and 1 hour south of Magdeburg. Leave Berlin very early in the morning and visit Quedlinburg, then either stay there for the night or catch a late-night connection to Hannover and then Amsterdam.
http://en.wikipedia.org/wiki/Quedlinburg
[ Edit: Edited on 21-May-2009, at 11:23 by t_maia ]