It’s fascinating to see that Germany has a very extensive beer culture with a whole set of customs, behaviours and rituals. For tourists it might be confusing, as waiters/waitresses will seem quite curtly a lot of the time, until you adhere to the customs or are in any other way found okay, then nothing is too much.
One of the things is the Stammtisch, according to Google translate ‘regular table’ in English. Don’t ever go and sit there by your own initiative. In Dutch we know the words Stamkroeg en Stamtafel but in those instances it’s mostly used by the customer who frequents that particular pub and always sits at the same table. In Germany the use and non-use of the Stammtisch is enforced by the establishment itself. You can only sit there when invited, otherwise the table will remain empty. Just as in the Netherlands it’s for the frequent visitors, but although I couldn’t get a clear answer on this, I don’t think you can just claim it for yourself after a few visits. I suspect that even as a frequent visitor, you have to be invited as well.
Another thing is the communication with beer mats. I haven’t seen it as much in Bavaria, but I know from experience it’s a custom in Dortmund and Düsseldorf. In a lot of the breweries and pubs in Düsseldorf, you can just get the one beer: Altbier. Latzenbier replaces Altbier during certain periodes throughout the year. Once you have a place at a table, sitting or standing, you get a beer mat with a beer on it and a pile of extra beer mats. On your beer mat the tab is generated. When you empty your beer, you get a refill and another strike on your tab. The only way to stop that is to put another beer mat on your empty glass, which says: I’m finished.
In Düsseldorf and Köln you get served by Köbes, an almost mythical race of waiters with a lot of legends surrounding them. They should be rough and surly as part of their reputation 😉 I am about to start in a book about them, so for now I won’t digress on this subject.
I noticed especially in Bavaria all personnel in classic beer venues tend to wear (mandatory?) trachtenmode. It seems to be the most favored uniform. Probably only in the more touristy places though, but I don’t think we visited a lot of other places.
Then there is the earlier mentioned Weißwurst which are traditionally not eaten after 12. This is supposedly because preservatives aren’t used in the preparation and the meat is not smoked, so when it’s made in the early morning, it should be eaten in the early morning, preferably together with a Weißbier, and of course the very sweet Bavarian mustard.
Probably most famous are the Biergartens though. Historically they were built on top of the beer cellars. Those beer cellars had to be kept cool, that’s why you can find chestnut trees on all biergartens: they have wide leaves early in the year and provide much needed shadow.
Which (other) German beer custom or quirkiness have you encountered?
Beer mats 
Weißwurst
Biergarten