Hey, I am a German, and I just ordered components for my own pc build from MindFactory. I don't have any experience with it, but I read a lot of good reviews about it. They sell at quite low prices if you use referrer links from a price comparison website (geizhals.de).
But I can recommend amazon.de as well. Personally, I would avoid MediaMarkt and Saturn since I find their products way overpriced. Aldi has a very low price for technology, but somehow I don't like their quality that much (good though, if you are at a low budget).
Unfortunately I am from the south of Germany, so I cannot quite recommend local shops in Berlin. I suppose an online purchase might be your best bet.
Thanks for the help.
My son isn't very technical (he's an English teacher). I like Amazon.de - but, I'm thinking he might get more help if he uses a local store in Berlin - in case there is a problem.