www.daad.de
The official site of the German Academic Exchange Service (DAAD). It has a mine of information.

www.higher-education-compass.de
Provides information about all state or state recognized higher education institutes in Germany.

www.bildungsserver.de 
Contains brief descriptions about all the courses offered in Germany and where these can be studied.

www.studentaffairs.de
Site of the Deutches Studentenwerk (DSW), a voluntary association of student organizations in German universities.

www.dfg.de/foerder/grako/liste.html
List of graduate colleges. This site is in German only.

www.germany-opportunities.de/study