The Kindle is great because you can store a ton of books on it and take notes and clippings from a book as you read it. The clippings get saved to a .txt file on the kindle that you can transfer over to your computer over USB. Your clippings from books you bought on Amazon are automatically uploaded to Amazon, but the books you didn’t buy from Amazon are not.

This is my workflow:

1. Read book and make highlights (enter book when started into “To Read” Google Docs Spreadsheet, transfer to “To Synthesize” when finished)

2. Copy My Clippings.txt file to Kindle folder in Dropbox

3. Open MyClippings.txt on the Kindle and delete all the old clippings so it is a blank file

4. Upload the copied My Clippings.txt file to http://www.clippingsconverter.com. This website is the best option for organizing your clippings. It is free. If you have a ton of clippings (over 3-4 MB) just separate your clippings into 2 txt files and upload them separately. The website can recognize duplicates so you don’t have to worry about being perfect.

5. Export individual books to PDF once I have finished reading them

6. Print PDF and 3 hole punch

7. Put Clippings in the appropriate 3 ring binder on my bookshelf and note its location in the spreadsheet.

I recently ran into a problem with the clipping function where a book I bought from Amazon had a clippings limit placed on it as DRM.

Use this to remove it:

http://www.ismoothblog.com/2012/07/calibre-free-drm-removal-for-amazon.html

then convert to .mobi and put it on your Kindle with Calibre.

You can read more about this issue here:

http://www.mobileread.com/forums/showthread.php?t=45427

http://www.amazon.com/forum/kindle/ref=cm_cd_pg_pg2?_encoding=UTF8&cdForum=Fx1D7SY3BVSESG&cdPage=2&cdThread=Tx25ST4BVWW2PDU