There are lots of lists of incubators around (eg please see OnStartups question 8614 ) however the majority are based in the US, with just a few in Europe.
(Please see OnStartups question 18887 for a list of startup companies that are based in Germany.)
Does anyone know of any incubators that are in Germany?
The Founder Institute now operates in Berlin. That would be the only American incubator, from Silicon Valley, in Europe.
Did you try googling? I got this result.
Wow, the answers here are ancient.
As of May 2013, the best way to find startups, events, incubators and investors in Germany is via AngelList - https://angel.co/germany You can also visualize them on a map - http://startupsbio.me/
There are many incubators, it depends also on the industry you're interested in:
Hope this helps.