Specific Judaica collections/portals:
RAMBI: Index of Articles on Jewish Studies
Judaica UB Frankfurt: Digitized Judaica holdings of Frankfurt University Library
Biblia Hebraica Stuttgartensia
Snunit: Seminal works of rabbinic literature in the original language (Mischna, Tosefta, Talmudim, Midraschim, Mishneh Tora of Maimonides)
Ketiv: The International Collection of Digitized Hebrew Manuscripts
Sefer Chasidim: Princeton University has digitized fourteen of the Sefer Chasidim manuscripts. You can use these sources by creating a free account.
Saadia Gaon, Sefer Emunot we-De’ot
Geniza fragments of the University of Cambridge
HebrewBooks: Over 45,000 digitized religious books in Hebrew, from various periods.
National Yiddish Book Center: Around 10,000 digitized Yiddish works – that's almost half of all the works published in Yiddish!
Jewish National Library – Digital Collections: Digitized manuscripts from classic Jewish literature and modern sources
Ben Jehuda Project: Modern Hebrew classics in full text
Heinrich-Heine-Portal: Digitized issues of works by Düsseldorf-born writer and poet Heinrich Heine with commentary volumes and lots more information about Heine himself (with a search function)
Historical Jewish Press: Digitized Jewish journals from the first half of the 20th century in various languages; full-text search option
Compactmemory: Over 100 Jewish journals from Germany, in full text, published between 1806 and 1938.
General collections/portals:
Europeana: Search over 58 million texts, images and artifacts from European cultural institutions
Gallica: Five million digitized texts, images and AV items from the Bibliothèque nationale de France
E-codices: Digitized manuscripts from Swiss libraries and collections