There's also this idea:
http://www.edukindle.com/2010/09/not...r-ideas-handy/
It just a simple trivial ebook file that you use with the Kindle's built-in annotation function. The resulting notes are in the usual place*.
*"usual place" = "\documents\My Clippings.txt" along with all of your other notes. I have this file listed in a "Reference" collection so its easy to find from the Home screen.