HubMed searches now have a link at the bottom of the page to submit your search to myOAI, a centralised search engine for Open Access Archives.
Currently the search returns results for BioMed Central, CiteBase, Humboldt University of Berlin, OCLC's Experimental Thesis Catalog and RePEc. Be patient, it can take a little while to gather all the results.
The Public Knowledge Project Open Access Harvester looks like it could be nice too, but there's not much indexed there yet.