I've lately been thinking about a trip to Berlin, but I want to go in summer this time - I've only ever been in fall, the couple times I've been there.

Let's see, late March? Will still be cold in Northern Europe, so a trip to a Baltic beach wouldn't be recommended. What about Bavaria - Munich or Nuremburg?

As to side trips excluding a flight (since you can probably find cheap flights to just about anywhere in Europe, ergo, why would you need advice, just get a calculator and do the math - LOL! ), when I did that Berlin-Prague in 1992, it was a LOOOOONG train ride. If I'm overseas for a short time, I wouldn't really want to spend a whole day commuting back and forth between Berlin and Prague on those trains, but that's just me - some people enjoy it, so whatever floats your boat (as they say).

Also, as I recall, the train from Berlin to Warsaw is about six hours and late at night. Don't know about a connection to Cracow, but Cracow is one of my favorite cities - it's very beautiful, and the Polish who live there are actually friendly, in contrast to Warsaw and other places (and I don't mean that in a stereotypical way, just in an anecdotal way).

You should be able to find plenty of day trip places, given the excellent transportation in Germany and how places seem to be crowded together...