Did an overnight in Amsterdam on my way to India. The trains run between central station and Schipol airport regularly and are a quick ride downtown. Once you get to central station there are hostels nearby (across street) or if you are to old for that, a Hilton right next to the train station which is very nice. Central station is walking distance to red light district if interested in hitting up some pubs and smoking stuff. The Anne Frank house is walking distance along with sex museum and the old town has some nice architecture and is pretty scenic.
There are also the Rembrandt & Van Gogh museums along with buildings that are older than our country.
I personally enjoyed the hell out of Amsterdam. I found a great Irish pub with a band every night and had a blast.
Munich:
Much larger city but again, train/subway direct from airport to downtown. IIRC it was about 45 mins travel time on train. I always stay at the City Hilton on Rosenheimerstrasse....the subway/airport train stop is below the hotel so very convenient. From the Hilton you can walk to a museum or take sub to next stop to Marienplatz which is the central square in Munich. Beautiful church/architecture right there. You can then walk to the HofBrau house for a pils.
Edit: Frankfurt sucks.... Depending on length of layover I would stay in Mainz vice Frankfurt. Frankfurt sucks.