The list might not be complete.

http://www.studienstiftung.de/stipendienprogramme.html
The foundation supports undergraduate and PhD students, junior scientists, junior journalists and artists. Nominations and self-applications are possible. more
http://www.sdw.org
The foundation supports undergraduate and graduate students. more
http://www.volkswagenstiftung.de
The foundation supports sciences and engineering, both in practical research and teaching. It aims to support research projects dealing with promising topics and to support institutions to optimize their working conditions. A special focus is given to junior researchers and the cooperation of researchers across borders between different disciplines and/or states. more
http://www.kalkhof-rose-stiftung.de/stiftung.html
The foundation supports scientists who have almost finished their „Habilitation“ theses (approx. one year prior to finishing) with fellowships and, in exceptional cases, also by covering expenses for materials or printing. more
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