Are Digital "Margin Notes" Possible Yet?

Stavo asks: "I'm looking for a robust, reliable personal knowledge management solution. As a professional researcher, I read a lot of text-based content. I prefer to mark up content, by underlining or adding margin notes. I also need to retrieve and search content. The low tech solution is printing the text and using a pen to mark up, then filing the papers. If I want to quote a source, I have to type the quote. With the advent of Tablet PCs and similar tech, I'd like to find a way to keep the content digital. In other words, if I download an journal article in PDF or HTML, how can I mark it up, save it, and later search/retrieve it? Shouldn't computers provide a better solution than voluminous file cabinets filled with dead trees?"