Thanks David,
after I uninstalled the language supplement for ArcGis 10.1, right clicking within the Python Window brings up the entry called 'Clear all'. And indeed it clears everything inside the window.
So the problem seems to be the Language Supplement (GER) that has a corresponding Term for 'Clear all' but doesn't work for any reason. If click it it will not clear anything but brings up another '>>' in a new line.
So is anybody experiencing that behaviour?
I will try to reinstall the language supplement, and will look if that will solve the problem, otherwise I'm going to use the English version.