The author of HubMed (an alternative and nicer interface to PubMed‘s database) recently posted an online journal review on his blog. While he prefers PDFs (as do I, for now), there are various aspects of articles-in-HTML that make them more or less useful and easy to read. All of the major publishers of online biomedical texts are scored. From the post:

HubLog: The state of online biomedical full text articles

I carried out a survey of HTML fulltext pages from the major publishers with the aim of identifying a) problems with usability and b) recurring themes in semantic markup of article elements (which will hopefully lend itself to a microformat recommendation for scientific, or at least biomedical, articles).

This is an issue on which the publishers are way behind. There’s little competition, and therefore little impetus for them to improve.