I discovered Mendeley today. Except for it's citation organization features, for which it is not unique (there are CiteUlike, JabRef and more) it works as a desktop app that indexes all your local PDF documents, and has an internal PDF viewer that lets you annotate the documents. These two are killer features that I've been looking for since a long time.
It's a pity though that it is proprietary. It would naturally feel better to put your work in the hands of an open system.