I have used the bibliographic database Endnote for 13 years, after starting out with another bibliographic database I no longer remember the name of. I take most of my notes in it. It installs with a link to Word, formats bibliographies, and lets you enter notes, including links to websites and locally stored PDF versions of articles. There are competing products around, but I think Endnote has the biggest market share. There are also open source versions being developed, such as Firefox Scholar.
Endnote is not open source and it is beginning to show some signs of limitations because it is a client-side application only, but I am happy with it. I would have liked to see a more flexible user interface, automatic links to Amazon.com or Google Booksearch, but it does have facilities for importing stuff from online databases, though I for one have never bothered to learn them (I only put in articles and books I read, so entering the bibliographic information is not that onerous.) Endnote is a better reference database than PIM, so a lot of functionality (cross-referencing between notes, for instance) is missing, though intelligent keywording can probably get around that. An excellent feature is the large community of users who have developed many "styles" for academic journals. This means that you can write an article, then format it afterwards into the style the journal wants.
I have more than 2000 books and articles, with notes, in my Endnote database, representing about 18 years of reading and taking notes (such as for this book). This is, to put it mildly, quite a resource for me – and I back it up religiously.
Recommended with the the usual caveats – it is not a web 2.0 product, but it has worked very nicely for me.