The list might not be complete.

http://www.daimler-benz-stiftung.de/cms/index.php
Each year, the foundation awards ten two-year fellowships to postdocs, junior professors or junior research group leaders, endowed with a sum of 20,000 Euros per year. The money can be spent on salaries for scientific assistants, on equipment, research journeys or on attendance fees. Eligible are applicants from any field of research who are somehow linked to a German university or research institution and running (or planning to run) their own research projects. Applicants should be 35 years or younger at the time the fellowship starts. more
http://www.dfg.de
The German Research Association supports researchers at every level of their scientific careers, both with individual funding and in DFG-funded programs, e.g., graduate schools or Clusters of Excellence. more
http://www.dmykg.de
The foundation awards prizes for the promotion of science, for the best poster presentation and for research, and a fellowship to researchers from the German-speaking area who are interested in mycology in human or veterinary medicine. more
http://www.henkel.de/karriere/stipendium-35559.htm
The foundation offers funding for PhD students at private and public universities as well as for postgraduate students planning additional and/or postdoc studies or internships abroad. In principle, the program is open to students from all fields of research, but the focus is on economics, social sciences, natural sciences, and engineering. more
http://www.ekfs.de/de/start.html
The foundation supports mainly clinical medical research, biomedical research, and medical-humanitarian projects. There are several fellowships available for physicians and natural scientists. Besides, universities can apply for funding of Chairs. more
The European Molecular Biology Organization awards fellowships (pre- and postdoc) to life scientists. Junior researchers about to start their own group can apply for a Young Investigators Award, scientists who want to move their labs to one of the EMBO member states can apply for an Installation Grant. In addition to that, EMBO offers funding for the organization of meetings, conferences, symposia, workshops, lecture series, and practical courses, as well as plenary lectures. It is also possible to apply for lecture grants and travel grants. Moreover, EMBO awards the FEBS | EMBO Women in Science Award to a female scientist who has contributed extraordinarily to the field of molecular biology and is a role model for younger female scientists. more
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