Anyway, here are three features I think an future, ideal such system should have:
A. co-location: notes should be inputable/viewable right next to the relevant source section. So underlining, adding margin notes and so should be possible in or in the context of the pdf-viewer, not (only) in a separate document in a separate window. And even additional notes in a separate document should somehow be (hyper)linked to the source text parts that they concern.
-Nod5
To do that, I use Word or OpenOffice "commenting" tool, and I have an older version of acrobat which allows to do pretty much the same thing with pdf files. Comments can be printed or not. I almost never print stuff -- unless I have to edit it for publication.
B. independence/portability: notes should be easily portable between different users, computers, operating systems, applications.
I find that the solutions mentioned above are pretty portable (between users, computers and even OSs —Windows, OSX, Linux). I have no trouble Reading my comments or notes in Linux, for instance.
C. systematicity: cross-document searching, indexing, tagging and so on of notes should be supported.
I use my own tagging system (that I've been trying to perfect a bit in the last few weeks : I simply use small textual abbreviations that I insert in comments, notes, file names, and that I use to categorise tasks, projects in Outlook or notes in EverNote), I use 2 desktop search programs (Copernic & X1) + Farr (see mouser’s section, here, at DonationCoder), and there are other applications I use a lot -- like EverNote, jedit, etc. As for the crosslinking-hyperlinking, I do it pretty much manually for now.
The secret for “success” is consistency and rigour... And I must admit I've not always been able to be up to the task. That's why I've been bothering people around the forum to find better ways to automate parts of my tagging system. I've trying keepass, tag2find, Clipboard Help + Spell, etc., etc., and I'm now comming back to AHK. We'll see.
Combining A-C seems like a very hard task. B seems to require some standardized format for such notes, a format that different applications can follow or at least import/export from/to.
It might be that I don't understnad you properly, but with X1, Copernic, Farr, the right tagging and file naming system, the right organization structure, the pretty standard "commenting" ability found in many software, and a good note taking software (myBase, EverNote, etc.), a good OCR program and a fast scanner, it doesn't seem like a terribly difficult task. Not easy -- one has to really think about all the different possible evolution of data, media, content, etc. -- but definitely feasible. I actually almost never use paper and my computer is pretty well organized. But I'm not saying there's no room for improvement !
One way to tackle this design problem would be to find an area with similarities to on-the-page note taking and that already has working solutions with features A-C. An interesting such comparison that I thought of is plain-text .srt-subtitle files for video: http://en.wikipedia.org/wiki/SubRip . These contain a list of paired timestamps and dialog text snippets. Put "movie123.srt" in the same folder as the movie file "movie123.avi" the subtitle was made for, start the video and chances are your media player will recognize and display the subtitle automatically.
Interesting. I'll have to check that : I'd like to “comment” video sequences...
Also, multiple notes for one single pdf file could potentially be combined and switched on/off individually, like layers in Photoshop ( http://en.wikipedia....igital_image_editing) ). Imagine a pdf viewer window with two panes. The left displays the pdf and also has a row of tabs/checkboxes on top. Someone studying ancient literature has a free pdf version of the Iliad. She then adds and compares on-the-page notes on the Iliad from scholar 1, scholar 2 and so on by clicking on the different note layer tabs. It would be as easy as browsing through the various audio tracks on a DVD disc! The right pane contains more extensive and general notes. Some hyperlinking systems connects these panes, so double clicking on a section in the right pane jumps the left pane the the related pdf section and vice versa.
Also, users could in the pdf viewer customize the display style for one and the same basic note file (like what a .css can do for a .html). For example, switch underline display color from red to green.
I'm not sure if I really get what you're sketching, but can't you already share comments by different authors in word or OpenOffice -- or even in acrobat, for instance?
Please forgive my English. Writing long posts is certainly challenging for me…
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