Alf Eaton has conducted two thorough surveys on the state of full-text articles in Biomedical journals. He's investigated content available as PDF and HTML, from a range of different publishers and sites.
Alf's conclusions show up some shortcomings in the way that content is published, in particular the lack of appropriate metadata that would enable researchers to better manage content in their personal libraries.
While IngentaConnect isn't explicitly covered in the review, you can be sure that we'll be taking these usability suggestions on board as we plan enhancements to our content management and delivery systems.
Enhancing of PDF content to include additional metadata (e.g. as XMP) and linking (e.g. to relevant data sources, not just references) is an area in which we've been conducting some research on recently.