Subject: Greece, Turkey, Egypt
I strongly discourage you to take the train from Germany to Greece, as it's an uncomfortable trip of several days, with very little comfort and a lot of bad people aboard. I'd suggest you take the train from Germany to Italy and then board a ferry at Venice or Trieste. Autumn schedule is about 3 departures per week and you can reserve accomodations ranging from a simple seat to a cabin with private bathroom. The ferries from Trieste are quite new, comfortable and affordable. The voyage takes about 36 hours from Trieste to Patra therefore, except in summer, it's not recommended to travel at open air on the bridges.

Paolo Trieste, Italy