Amazon will keep a backup of all books you purchase from them, as well as bookmarks/notes/highlights/last page read which can be re-synced from the new Kindle provided you have the old one set to Backup Annotations in the settings.
You can easily re-download all your titles either via Whispernet, or directly from the Manage Your Kindle page on their website.
Your non-Amazon books you'll have to backup and transfer over yourself, and also the associated .mbp, .tan, and .plr files which keep the bookmarks etc. locally for those books.
You should also probably save a copy of your MyClippings.txt file manually, although I think the new Kindle might possibly regenerate it from the existing highlights when your books are copied back.
There's a way of transferring collections, which are not automatically carried over. One is detailed in the user guide which provides much better instructions about that I could. The other involves copying the .json file, which apparently houses info about one's collections, over manually.
Hope this helps.
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