Thanks for this list! I subscribed as soon as I heard about Tor's generous offer, but missed a few of the early ones. Now my list is complete.
I haven't used Calibre but for my Sony Reader, I download in html and use the Word template I set up (according to Sony's instructions) for creating a PDF that's formated for the Reader's screen. So far, it has worked nicely and doesn't take too long. (It's not set up for batch files, though, so I'm sure there are faster ways out there to convert a lot of books at one time.)
Html seemed the most versatile format to me, since I could easily reformat it to fit whatever device I wanted to read the ebook on.