Science Commons: this is the central "clearing house" of everything to do with Open Source science and scientific research.
BioMed Central:an independent publishing house committed to providing immediate online open access to peer-reviewed biomedical research.
PLoS One: the Public Library of Science is a non-profit organisation of scientists and physicians committed to making the world's scientific and medical literature a freely available public resource that publishes peer-reviewed research online. Two links here - one to the library and one to the organisation. Directory of Open Access Journals: aims to increase the visibility and ease of use of open access scientific and scholarly journals thereby promoting their increased usage and impact.It aims to be comprehensive and cover all open access scientific and scholarly journals that use a quality control system to guarantee the content.A one stop shop for users to Open Access Journals.
A good article on Open Access research by John Wilbanks of the Massachusetts Institute of Technology pusblished in the British Medical Journal is here.
I think I'll start a Links section dedicated to Open Source medicine and science.