Guys, Kindle 3 note making is very comfortable (not familiar with Nook Touch, so cannot comment), 5-way joystick moves cursor steadily and fast.
One problem still persists: Notes in My Clippings.txt are placed by date, so if you read two or three different books, jump between books and make notes/highlights - it will be PITA to get notes from one book only.
Small tool developed by user of the-ebook.org will help you to extract any selection from My Clippings.txt.