An excellent link collection:
http://www.amherst.edu/%7Eedstarr/judlibs.html

Homepage of the Heidelberg "Zentralarchiv" (German version)
http://www.uni-heidelberg.de/institute/sonst/aj/index.html

Peter Honigmann's article "Die Akten des Galuts" on the history of Jewish archives and the inventarisation of Jewish sources in Germany is online:
http://www.uni-heidelberg.de/institute/sonst/aj/B6/galut.htm

More Jewish resources (too small list):
http://www.stub.uni-frankfurt.de/webmania/ljud.htm

One must add "Compact Memory" - digitization of historic Jewish Journals in Germany including the "Mitteilungen des Gesamtarchivs der deutschen Juden" (1909/26):
http://www.compactmemory.rwth-aachen.de/cm2/html/

Online texts related to Jewish History
http://jewishhistory.huji.ac.il/links/texts.htm

Databases for academic Jewish studies
http://jewishstudies.virtualave.net/Other_Internet_Resources/Databases/index.shtml

RAMBI - Index of articles on Jewish studies
http://jnul.huji.ac.il/rambi/