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I would get one of those 'journal' ebooks from the Kindle store (most are 99 cents) to collect and organize your notes. Your annotations will be accessible on your kindle.amazon.com page, and synced between Kindle devices or apps that are registered to your account, and have the 'journal' ebook downloaded.
I'm sure there are plenty of rich text web editors that work with Kindle's browser as well, but probably it is not going to be as usable.
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