Both Berlin and Prague are worth five days easily. If you want, you can travel to Dresden as a day trip. There's enough to do for a full day in the pedetrian only Old Town, and you might even consider staying there overnight to give you more opportunity to explore. It's on the train route from Berlin to Prague anyway.
Prague has a number of good day trips, including Kutna Hora and Karlovy Vara. Cesky Krumlov is theoretically possible as a day trip, but it's about a three or four hour bus ride each way, so you need to leave early in the morning and come back late. Frankly, I'm not the biggest Cesky Krumlov fan. It's quaint and lovely architecturally, but absolutely overrun with tourists. It's being loved to death, in my opinion. I wish I had been there ten or fifteen years ago.
Munich is definitely worth a visit, and if you drink beer, you owe it to yourself to try some Munich brews and compare them to the superb (and far cheaper) beers in Prague.