Tony,

Seems like no one can answer your request -- probably because you're asking too much. I don't know any program that does all this. I've added a few suggestions among your questions below:

TonyJ wrote:

My tablet came with OneNote, so far it looks like a good piece of software. Do I need a
combination of programs to do it all, or is OneNote sufficient? Here's what I'd like to
be able to do:

1 - Annotate ebooks, preferably in ink. Mostly .pdf or .djvu. Perhaps
other formats in the future. Link from a given paragraph of one document to a selected
paragraph of another. I think OneNote can handle this.

I'd say ON is the best bet.

2 - Store all my email. My
email is on an IMAP server. An offline backup where I can link emails to a list of
contacts and tasks (and link them back to the emails) is ideal. ON - not as far as I can
tell.

3 - As implied in 2, keep a master list of contacts, and manage my projects and
to-do lists with a calendar. A good fit with GTD would be ideal but it isn't necessary.
ON - ?

Take a look at Debrief Notes. (www.debriefnotes.com) It tooks a little bit of work to figure out the GUI but once you do it makes sense and is pretty powerful.

4 - Accurately save web pages. Saving the entire site isn't necessary but Web
Research's feature of allowing the user to save some of the pages linked to is very
nice. An editor where I can cut chunks out of the webpage and eliminate animations,
banners and ads would be a strong feature. Ability to export as an html or mht file is a
plus. ON can import them as a screen capture but my preference is for the links to work.
Linking to a specific section in the web page from an external document is another
plus. ON - ?

Many people like Surfulater for this task. (www.surfulater.com)

5 - General note taking. ON does this very well.

6 - The more easily I can
use ink, the better.

Debrief does ink, but I haven't tried it.

Linking documents and annotating in ink are the two big wants,
but none of this is written in stone. All the linking between different types of
documents (email, .pdf, .doc, .jpg, etc.) suggests one database to hold the whole
thing. UltraRecall and InfoSelect are getting my attention. Web Research also has
some strong features but I don't know if it can handle a big database and I expect some of
these OneNote files holding printed text books, will be rather large. What about SQL
Notes? I hear that scrapbook is a free way to save webpages. Are they saved as html? If I
used scrapbook is there a good, maybe even free, database for organizing and
annotating them, which I can then link to the ON pages?

OK, that's a lot of questions.
Thank you for your thoughts.