In my line of work I tend to read many document, comment on them and then summarise them or take extracts from them.
In the past, I used to print out the documents, scribble my thoughts and comments in the margin, and add plenty of arrows and circles. I'm awful at keeping my workspace tidy, so there are many documents scattered around me, so I tend to spend hours trying to locate the right document. I also go through phases of "lets de-clutter", and throw away plenty of paperwork and documents, only to realise in a month's time that I've thrown away valuable notes.
Recently, I started writing my notes and comments in a txt file. So whenever I have a comment to make about a paragraph, I list the page number, paragraph number or table ..etc and then write up my comment. Some people use Excel sheets for the same purpose.
The downside to this is that you lose the visual connection. The scribbling method allows you to insert visual cues in the document, and that in itself allows you to recall your thoughts and also important parts of the document that you would want to constantly refer to.
So I've been thinking, why not develop an application that allows you to create a "scribble" file. Whenever you open a document (e.g. pdf, doc, ppt ...etc), or maximise any window (so you can scribble on web pages if you like), this application would ask you if you want to scribble, and if you do will open for you a transparent layer on top of the window containing the document. The application should have a suit of drawing tools, so you can scribble, draw circles, arrows ...etc. When you're finished, the application automatically saves the "scribble" file and links it to the document file.
This can be easily developed for a start, but it gets more complicated if you want to link the scroll bars and zoom areas of the document viewer and the "scribble" application. This is a necessary thing if you want your scribbling to be aligned to the text the next time you open the document and the linked "scribble" file.
Until someone develops such an application, I have to live with my pre-historic put-your-thoughts-in-a-txt-file approach.