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Bryan's list of databases on the WWW (created: 2007-09-01)

Science databases in the deep web (Gary Price)
-- I had previously linked over to Gary's website in my 2007-06-21 Slashdot post.

arXiv.org- Open access e-prints in Physics, Mathematics, Computer Science, Quantitative Biology and Statistics
Directory of Open Access Journals (DOAJ.org)

Review literature in high-energy physics (HEP)

PubMed Central

Wikipedia:List of online databases
Lifehacker's "Where the web archives are"

AutoScholar - perl scripts to help automate the retrieval of PDFs etc.
2008-04-21: http://pubget.com/site/search streamlined version of pubmed, you get the pdfs right away (by way of Ricardo Vidal on the oww mailing list).