Chemistry Central is a sub-set of BioMed Central. It features articles from journals that are peer-reviewed and open access.
Defining open access journals as “journals that use a funding model that does not charge the readers or their institution for access,” the DOAJ aims to be a comprehensive listing of open access scholarly journals that use a quality control system to guarantee the content. Journals can be located by title or broad subject.
This list contains links to chemistry journals that are "permanently" free and online. There are also a links to trials and temporarily available chemical journals, and chemistry journals in Russian.
A list from PhysNet of physics-related journals which are freely available on the Web.