I thought it might be worth starting a new thread, since my reply elsewhere
was getting a bit wordy....
I've been using Scrapbook
(a Firefox extension) for about a year now. It saves whole webpages (with their images and stylesheets etc), each in its own (non- proprietery, and so easily searchable with other tools) directory. The directories have id names (based on date created), but Scrapbook indexes the URL and date created, as well as other meta information you add (a title, comments) and displays the pages within a Firefox sidebar, in a searchable simple outliner/hierarchical list, which is quite easy to arrange and modify.
You can edit the page before saving it (using a Dom Inspector
style interface), and add embedded sticky notes, highlighters and tooltips. You can also save only that part of the page you've previously selected, or choose not to save images/sound files etc.
You can choose to capture linked pages (to the depth of 4), although I don't think it compares well in functionality with specialised offline browsers like HTTrack
It supports single notes too, which appear in the outline as single entries. Also bookmarks, although I don't find it a useful interface for bookmarks (that have no saved content).
One very cool feature is that it's easy to combine a selected group of saved pages and notes into a single (long) webpage. I use this from time to time to pass on "findings" to someone else, since there is very little extra time needing to be spent on organisation of the information. It can also export a group of webpages organised into its own folder with an index html page pointing to the other saved pages, which again is useful for passing on information to other people.
Caveat: with all this saving each page into its own folder, you can too easily create unwieldy "scrapbooks" of thousands of small files and directories, which are a pain to backup or use on a portable drive. For this reason I've changed my habits with it; I save less than I used to, and I purge pages from completed projects. However, when I really need it it's wondefully simple, functional and accesible, right there within my browser, always at hand.