In Berlin, my favorite pipe shop is Der Pfeifenladen, very friendly and you can get lots of information about the pipe and tobacco scene in this little Europe. You can find Germains there sometimes, but the 10+ tins will be gone within a few days. The nearby shop, Tabak & Pulver focuses more on cigar, and the interaction is less personal, more professional - you can find John Aylesbury there, I never tried it, but I just know that they sell them overseas.
When you are in Germany, if you fancy HU Tobacco, you can order them online when you are in Germany, and then send them back home first using Deutsch Post - declare it as whatever you like.
If I have to recommend one or two places to visit for tobacco in Germany, it will be these two:
1. Herbert Motzek in Kiel
Mr. Motzek has retired last year, but he found a successor for his shop and blends and secret recipes over an extended period of search. The shop and its new and old products are still renowned in the whole Germany.
By the way, "Motzek Strang" came from this shop, so differently try their house blends.
http://dein-tabak.de/
2. Peter Heinrichs in Bergheim (or Köln)
The shop is most famous among pipe-smokers in Germany and is known as the "Haus der 10.000 Pfeifen" (House of 10000 pipes) as the now passed-away (last year) owner Peter Heinrichs started the shop out of his passion of pipe smoking and pipe collecting.
Chateau Henri