arXiv - Front end for the Mathematics portion of ArXiv (e-prints and pre-prints) from UC Davis and Cornell
CiteSeer - also known as ResearchIndex, this offers searching and links to computer science research articles posted on the web. It also indexes citations from those articles. It was originally developed by staff at the NEC Research Institute.
HAL (Hyper Articles on Line) - Multidisciplinary article server under the auspices of the CCSD (Centre pour la Communication Scientifique Directe, France)
TEL (thèses-en-ligne) - Multidisciplinary theses server from the CCSD (Centre pour la Communication Scientifique Directe, France)
Sites with Everything
Mathematics Digitization - bibliography with links to major online collections of mathematics and statistics, compiled by Steve Rockey at Cornell University. Some are freely accessible, some subscription based.