We are taking a Viking River cruise from Nuremberg in October. I can fly to either Munich or Prague before the cruise for 3 days, then will take a train to Nuremberg. The train form Prague is 5 hours, the train from Munich is 1.5 hours. Which city would you recommend to spend 3 days?

Without a doubt Prague.

No question - Munich!

I'm not sure where your cruise takes you so I'll assume it's mainly Germany. That being said, go to Prague. It's rich with architecture, history (old and new) and a relatively new political scene that's so different from what you'll see in Germany or Germanic countries.

Personally, without the cruise, I'd go back to Prague in a heartbeat and I thoroughly enjoy Munich.

It all depends on your interests.. history? architecture? beer halls? museums?

The new political scene in Prague is a catastrophe. Not recommended to even have a short look at it (unfortunately I have to b/c of job reasons).

My vote for Munich. You could even make a day trip to the Alps (Garmisch).

I vote for Prague, although I really enjoyed Munich also.

Having been to both I would say this: the "political scene" in Prague cannot be any worse than the one in the US and THAT hasn't made a visit here any less attractive so I'd discount Ingo's remarks if I were you.
Both cities are wonderful in different ways...Prague will seem much more "old world" and medieval than will Munich but both offer many sights: Munich has the Nymphenberg and The Residence; Prague "the" castle; Prague's "old town" is a delight for baroque lovers not to mention the Charles Bridge, Wenceslas Square, etc. The countryside around Munich with Neuschwanstein, Linderhof and also Berchtesgaden...easy day trips. You cannot go won with either city in my opinion.
A word of caution: if you go to Munich mainly for the "beer" experience you'll be selling it, and yourself waaaaaay short. Have a great trip.

Well I know both cities quite well and I think there are a couple of factors you need to take into account when making this decision.
1. They are both very beautiful cities, but Prague has more historic especially art noveau and medieval architecture.
2. Munich is more diverse like most Western European cities and a far wealthier i.e more expensive city than Prague. Because of its wealth Munich has more world class museums, shops and (expensive)good resteraunts with international cuisines.
3. Munich has a far more beautiful countryside that is easily reached with public transport.
4. Prague's center districts have more old world charm and mystery but Munich has plenty of quaint neighborhoods and a good mix of historic and modern buildings.

I personally prefer Munich because I find Prague has a bit of a harder edge that I dislike (aggresive taxi drivers, drunken unemployed men in the center, dirty subway stations, tourist traps). Also Prague is far more dependent on tourism and the city center is full of tacky discos and adult clubs catering to foreign tourists. The people of Munich are also seem much friendlier to tourists than the people of Prague, at least in my opinion. I find Munich more pleasant and it seems to be a more confident and comfortable city.

But having said all that it depends on what you are looking for. Munich wins hands down for a family vacation and a relaxing time but Prague is probably more appealing to students or young travelers and architecture fanatics. Another deciding factor may be cost and Munich is an expensive city with Northern European prices, Prague is far cheaper and you will get more for your money.

I've never been to Munich, so perhaps it's unfair for me to post, but Prague is such a wonderful city I just had to recommend it to you. We visited there for the first time last spring and can't say enough good about it. The whole feeling and atmosphere of Prague is wonderful. We loved the food/beer, the museums we visited, the castle area, the people, who were friendly and helpful and many spoke English which was helpful.

So much to see and do. We can't wait to return.

I have been to both of them and love them both! you can't go wrong either way. The best part is if you like the beer in Munich, I actually like some of the beer in Prague better! especially the Krosovice or the PilsnerUrquell but the Munich beer is still as good as its reputation.
Cant you go to one city and return from the other? We are planning on seeing both of these cities again this fall. Have fun

Thanks to all of you for your tips. I still can't decide. The cruise goes from Nuremberg to Budapest, so we fly home from there. We will spend 3 days in Budapest after the cruise. Is Prague similair? So maybe Munich will be the bettter choice. Beer doesn't factor into my decision, but I do speak some German which may make it easier to get around in Munich. We like castles and art, not into high end shopping.
Any more feedback? I have to let the airline know today which city to ticket me to.

Budapest is more similar to Vienna than to either Prague or Munich. Prague has much more of its medieval architecture than Budapest and is a smaller city.
You might just have to flip a coin but really, you can't go wrong with either city.
One final recommendation if you are going to Budapest but not Vienna, I would definetly choose Munich because that way you get to see a large Eastern European city and a Large Western European city. Prague and Budapest aren't bad but you will see more differences between Munich and Budapest.

Good luck

We will be in Vienna, but only for 1 day on the cruise. Plus I have already been there, 10 years ago. Another concern about Munich-we'll be catching the tail end of Oktoberfest which may make it difficult to get a hotel. or is this not an issue?

My vote goes to Prague, no doubt! Munich meant nothing to me.

Well, after doing some looking for hotels in Munich for the last weekend of Oktoberfest, there is NOTHING available at under $100 a night. So I guess the decison has been made for me-it will be Prague we'll visit. We'll visit Munich sometime when it's not Oktoberfest.