I have a personal wiki that's powered by Org mode.[1] My wiki contains around 1,000 documents, including all my notes and personal task lists.
I've stopped using bookmarks, other than smart keyword bookmarks[2] in Firefox. I previously had thousands of bookmarks. I now use my wiki for long-term storage of URLs, and I use a feature-rich Firefox extension named Session Manager[3] for short-term storage of unprocessed URLs that relate to topics I plan to study in the future.
Before I started using a personal wiki, my notes were stored in files of various formats, and the files weren't linked in any way, which in retrospect is crazy because many of the subjects I've studied are very closely related.
I can't imagine not having a personal wiki at this point, and almost immediately after I created one, I strongly regretted not doing so sooner.
At some point, I plan to convert my notes from Org files to HTML so I can publish them to the web. I plan to use Middleman[4] to create the site template because I like Haml and Sass. I just need to find the time to identity all the sensitive information in my notes so I can filter it out before publishing the documents.
EDIT: I use a small paper notepad and pen for notetaking when I don't have access to Emacs. I process the notes on my notepad daily.
[1] http://orgmode.org/
[2] http://support.mozilla.org/en-US/kb/how-search-from-address-...
[3] https://addons.mozilla.org/en-US/firefox/addon/session-manag...
[4] http://middlemanapp.com/