For a separate list of math blogs and forums see math blogs. Main wikis should belong to both lists. For math societies and institutes see math institutions. There is also page of math resources by individuals. The level up is math resources.
We list archives of online books, not the catalogues of physical libraries. We shall not list commercial subscription lists (especially of current journals) except semi-commercial jstor and few publication sites by the main mathematical societies.
arXiv archive of free preprints (math, physics, computational linguistics)
spires high energy physics publication database
The SAO/NASA Astrophysics Data System (it also contains abstracts, scans, citations of many papers in mathematical physics)
Hopf archive topology and K-theory
ICM archive past ICM proceedings
project euclid list of journals (colors denote levels of free access)
huge MPIM list of electronic journals – most are available only locally, but many free ones listed as well
lib.mexmat.ru Moscow MexMat electronic library: most items available only locally, however some items and the indexes are available
Aarhus math institute, preprints and dissertations
encyclopaedias in Russian online: dic.academic.ru
Math on the Web links maintained by American Mathematical Society
fsu vmlib Florida State University Virtual Math Library – long list of resources