I have used Endnote for at least a decade as my primary bibliographic tool, long before it was acquired by Thompson Reuters. If the reporting of a lawsuit brought by Thompson Reuters is correct, then as an academic community we need to seriously reconsider our prior recommendations of the use of a product that seems to now be configured precisely against the emerging fluidity of referencing and hyperlinking encouraged by the web from its outset.
One of the widely recognized successes of the Web was indeed in its dissemination of several decades of developments in hyperlinking that allowed, among other uses, different sources of knowledge and information to be hyperlinked. The occasionally wobbly efforts in deploying a Semantic Web that includes some minimalistic formalism of knowledge representation constitute an important and worthy attempt to make such hyperlinking and annotation even more efficient and productive. So, when Thompson starts suing open sourced efforts (using Semantic Web standards) to interoperate with the Endnote bibliographic styles, it is (again if the reports are accurate) creating obstacles to the free flow of information between the richly growing ecosystem of reference and bibliographic applications (web-based or otherwise). This runs counter to all the trends in open source publishing and widely shared document formats.
If indeed, I have misunderstood the nature of the lawsuit then I will readily and publicly retract these comments in this forum. Otherwise, those of us who want our students and colleagues to be able to freely exchange their bibliographic data will consider some alternatives.