I've been lucky enough to have had 2-3 business trips to Germany and Austria for about ten years, so I've had opportunity to sample a lot of different types of offerings in both countries. I can confirm what others have said about Austria. It's definitely more expensive for pretty much the same quality of experience. Also, the options are much more limited. In Vienna, there are only three FKKs in the entire city. In Germany, there seems as if there are three FKKs on the same block in a lot of cities. I've not tried it in Germany, but the FKKs in Austria will sell you the generic Viagra gel for EUR 10 a pop. The "flagship" FKK is Goldentime, accessible by S-Bahn. The optics are similar to Artemis, but it's a much smaller establishment. It has a outdoor area which is great on a warm summer evening. Lesser-quality FKKs are Funpalast and Fresh. Other unique places in Vienna are Maxim (a combination strip club and brothel) and Babylon, which is a high-end elegant brothel in which you can have a full-course dinner with your chosen one before heading off to the room. Be prepared to spend about EUR 500 at Babylon. There are tons of studios and laufhauses. The studios usually have 3-4 girls and are barebones places. If you're really adventurous, you can dive in without a raincoat for a small upsell. Laufhauses are basically indoor red light districts.
Berlin pretty much has everything you would want to try. I would save the money you're planning to spend to go to other cities and spend it on the girls. Berlin has a top-notch FKK (Artemis) and a couple of flat-rate clubs. (I've been to Airport Girls. The girls aren't as attractive as what you would find in Artemis, but, my experience is that they enjoy sex a lot more. There are a few sex parties/gangbangs. I've been to a few, but certain guys who are veterans to this scene can shut out the visitors. For the GBs, you need to be comfortable with public sex and sharing a large bed with 2-3 other couples. There is also a streetwalker scene which is worth a look just to blow your mind. The U-Bahn and S-Bahn will get you to all of these places.
I know I approached this from a cost and availability point of view. Given that you are also traveling for vacation to Vienna and Munich, you certainly can't go wrong in any of those locations. I've pretty much hit everything in Vienna. There isn't a lot in Munich itself, so you will definitely need a car. There is an FKK Coliseum in Augsburg, about a hour's drive from the Munich airport. It's in the Artemis class.
Bring a fully-loaded ATM card and get plenty of sleep!