Sven from Simplicityblis has a very insightful post about the intersection of Evernote GTD and reference files. His main point is that Evernote isn’t best at being your task manager although some seems to have done made it work like one (see Daniel Gold’s ebook or The Secret Weapon site. Where Evernote excels is storage of support and reference materials. Search, tags, notebooks, ability to index PDFs, audio and photo storing make it very powerful archive.
I would agree with Sven and this is how I now use Evernote. I Initially used it for content creation, storing ideas, research etc however since I moved to plain text for most content creation needs and list keeping using Evernote became much simpler. Before I blended various types of work and content now I have a nice and clear division between creation tools and storage/archiving.
Sven’s post: On Evernote, GTD, Reference and Support Material