You might want to take a look at
wikindx which is a Virtual Research Environment with support for EndNotes. There is a DokuWiki plugin,
wikindx, for it.
You may also find the
docsearch,
yabibtex, and,
bibtex plugins useful.
Adding annotations to the original pdf is interesting, I'm not sure how you'll manage that but I'll be interested in reading the results. Have you considered not putting the annotations into the pdfs and just linking instead?