Scrapbook is a Firefox extension which allows you to capture portions of websites or the entire website and store it locally on your machine, where you can then search the contents, make notes on them, and organize them as you see fit. It’s free and is good at what it does.
I’ll confess that I don’t really buy the use of the browser as a scrap booking tool. I’m doing similar things using Devonthink Pro though (capturing the full contents of websites along with snippets from them) as a knowledgebase tool so I understand where this is coming from conceptually. It just seems to me that lacking some of the intelligent filtering that Devonthink provides this isn’t nearly as useful. Still, many folks seem to use and like it. Maybe you’ll become one of them.