I think I can address some of what you requested using UltraRecall (http://www.kinook.com). Here is how...

UR has a feature that I have not seen in any other PIM system. It allows you to link (or store) any document on your system e.g. pdf, doc, xls, OL items, anything. You can actually store the doc within UR database and delete it from the OS. Once done, you can, then, decide to edit this document internally within UR (using its native RTF editor), integrated IE based browser, or externally using the doc's associated default program. Even if you edit it externally, you are still editing the internally stored document. The unique feature is when you save your edits, you can synchronize it and propagate your changes to the doc that is stored in OS folders. If you edit the doc on the OS, UR will see the changes and update its stored doc accordingly, so this is a 2 way sync. Some users keep all their files on the OS, link them into UR for organization, and sync. Some keep a copy inside UR, and a 2nd one on the OS, and keep them in sync. This way they have 2 copies of any given doc all the time.

This feature is great by itself. Furthermore, you can benefit from UR system generated keywords when you link or store a doc. You can also define your own as you wish. The level and complexity of the tagging system is all dictated by you. searching is as-u-type, fast, can be saved, and is very customizable.

As fas comments and notes, UR associate a note page with every doc or item. This note is specific to a single doc and can be displayed right next to the doc itself and resized.

Commenting on PDF docs was something I did all the time using AcrobatReader Pro 5. It did the job beautifully. You can add notes and even make changes to the actual text of the pdf. Armando pointed to the same thing. I also used a product called RepliGo made by cerience.com Simply but, you can print any pfd document to a RG document via its virtual printer driver. You can read it in RG and highlight whatever you like. Each highlight is a comment where you can add your own. You can then view all comments in a doc as a summary. RG is optimized for small screen and use it all the time on my Treo. It is the best solution I've seen. However, it has not be developed in ages and I'm not sure if the company is still interested in maintaining it.

Hope you find this helpful.

Mouser,

your coding ability amazes the hick out of me. You probably write c++ as spontaneously as we speak English if not better. I would pay a million dollar to have your knowledge transplanted in my brain.
You must've also inherited a million dollar to have you do all this work of managing the site and writing code voluntarily and on donation basis.
If you ever decide to write your diaries, please let me know. I will be the first one to read them.

Thanks for brightening our lives with your ingenuity