I can't give you any tips directly for Berlin, but general tips:
Have a gynecologist you're comfortable with and trust. They'll give you a little booklet called a Mutterpass which keeps track of pretty much everything during your pregnancy.
It looks like this (DON'T LOSE IT, by the way!! That would be bad-- take my word for it!):

Later on you'll be recommended to a Hebammer (mid-wife) who will help you towards the end of your pregnancy to prepare for the birth, choose a hospital, etc. I'm sure you'll have a load of options, but these were the people who were the most helpful to me during my pregnancy. If you don't speak German, go for English speaking doctors/midwives (obviously).
A short list of English speaking ObGyns in Berlin.