Prague Sidetrip -- what has your vote?

Dresden can be done as a day trip easily from Prague. Kutna Hora is a very easy day trip from Prague only an hour away. Munich and Salzburg would need an over night but If I had only one to do an overnight in it would be Cesky Krumlov. Can be done as a day trip from Prague but better as an overnighter.
you could also consider Tabor and Karlovy Vary as possible day trips from Prague too.

One night... Cesky Krumlov would probably be first choice also. Charming, fairytale village perfect for wandering about and seeing the sights. However, you could also do Salzburg and get a taste of the Sound of Music area:) It is also quite walkable and if you are not planning to visit this area again it might be a good time to give it a day. I would look at travel logistics and see which would be easiest and make the most sense. I don't think you can go wrong with either .

We are in Cesky Krumlov now, staying 1 night and after 6 days in Prague, a perfect relaxation day, just walking around, taking in the sights and you can't take a bad photograph :-) A stunning and beautiful Czech town, every bit as great as they say.

We took the Bean shuttle, an easy 2 1/2 hour trip.

Gene

Without minimizing how nice it is, Cesky Krumlov can easily be "done" in a day-out, with early departure (DO NOT take the train, it's the slowest option). The big cities you name can't be done in a day-out. Even a single night short-changes them. (Opinion)

I would also opt for Cesky Krumlov, and an overnight would be perfect. It is indeed a fairy tale type town and perfectly tailored for aimless, happy wandering. I think that it would provide the biggest bang for your daytrip buck. We have been to all the towns you mentioned, and IMO while you could do a day in any of them if you chose, CK would be the most rewarding and not leave you feeling "Gosh, I wish we had more time here." The logistics would play a large if I were choosing, weighing in travel time vs time in town. KH is even easier to reach by Prague than CK, but we found that despite our earnest effort, we finished the bone chapel in about 15 minutes and the town, while nice enough, was nothing particularly special, particularly after Prague. A shuttle may be available from the bone chapel to town, the chapel itself was a very short walk from the KH train station. I think it is the most doable day trip without overnighting. In CK we stayed at the Hotel Konvice and were pleased with a nice room and excellent breakfast buffet. Quite close to the main square and several nice restuarants and TI office.We also took a wonderful canoe ride down the Vlatava. A lot of fun, very easy paddle, and a few minutes walk from town center to livery. At the outset it's like Chutes and Ladders, water style. Several trips are offered; we took the route suggested by the canoe lady. Midway along the river we stopped for a beer and grilled lunch, at the end they pick you up and drive you back to town. We were there in early, mid May and the river was quite shallow..an added perk for for someone like me who gets nervous in a bathtub. Have fun wherever you choose.

I also vote for Cesky Krumlov. Rather than just a day trip stay overnight. The best way to get there is by Student Agency bus so called Yellow Bus. Yes it's yellow. Second best - Kutna Hora. Nice relatively untouristy medieval town with rich history. Doable from Prague without overnight. Most people see Ossuary, cathedral of Santa Barbara, silver mines. You can find more information about Kutna Hora and Cesky Krumlov in Rick Steves book: Prague & the Czech Republic and I recommend these websites: http://whc.unesco.org/en/list/732
http://www.czechtourism.com/t/kutna-hora/
http://www.outsideprague.com/kutna_hora/kutna_hora_daytrip.html
Munich and Salzburg are too far for a daytrip and especially for Munich even one overnight would be too little. Although Dresden is not as far, it's a relatively big city and just one overnight would not do justice to it.

As a day trip from Prague...Benesnov.

Benesov is really close to Prague. Most people who travel there just stop briefly on their way to nearby Konopiste castle (or chateau or something between castle and chateau). Read about Konopiste in R.S. book Prague & the Czech Republic.