I have been playing with Sigil to clean up a Gutenberg book and have gotten very comfortable with it. So I decided to use it to make a nice book out of my Kindle clippings so they don't just sit there growing longer and more disorderly
I find that since I read more than one book at a time, I need to reorganize them anyway, and I'd rather have it in a nice format than all jumbled!
So, I made a Sigil file using the tutorial
here. Chose a cover image off Google Images, added a title and set the whole thing up. Then I made sections for each letter of the alphabet (A-B, C-D etc.) Then I just copied the clippings file to my computer, opened it up and started cutting and pasting in the text, alphabetical by author's last name. The great thing is, if I had something later in the file but from the same book, I could just paste it into my file at the right spot and I would have a sequential record of the book.
When it was done, I loaded it into Calibre, converted it to Mobi and voila! When my clippings file gets long again, all I have to do is open up the epub again, make my edits and load it back into Calibre.