It won't quite get everything, but you could use a combination of
Zotero and
PDF Xchange Viewer. Zotero is a fairly powerful citations and documents manager plugin for Firefox. It also allows you to annotate .html and .txt files (it's not the greatest annotator in the world, but it works), and you can attach separate notes to each of the books/articles you have stored in your database. It will even sync all your stored citations and txt/html/pdf files online. It's miles ahead of Endnote, and it's free.
For viewing .pdf files, Zotero uses whatever program Firefox normally calls up to view .pdf files. I use PDF XChange Viewer because it allows me to highlight text and write notes in the margins and it's free. It adds another layer on top of the .pdf text which will show up in other programs like Adobe, but they can be deleted again from within PDF Xchange Viewer itself. You might want to double-check that PDF XChange Viewer does not place marks at the top of a document when you print it out--I really don't think it does (I believe it's Foxit that does that on their free viewer), but I forget since I don't print .pdfs very often. It's a powerful combo. Throw Microsoft Reader in there for (easily convertible) .lit files, and yes, you have quite the document management system.