My Calibre library is kept inside my
Dropbox folder. It backs up automatically to a web account. You can get two gb for free and if you sign up using the link I gave, you (and I) get some extra space
I would not reply on the 'cloud' of the bookstore. I had some issues recently where I had to re-download some books but since they were no longer for sale by Fictionwise where I bought them, they would not let me download then again. It took awhile to straighten out and left a really bad taste in my mouth.
I like Dropbox because it is a no-brainer. Whatever is in that folder gets backed up and I don't have to think about it. When my hard drive crashed, it was very easy to get things up and running again, I just downloaded the folder, told Calibre my library was there, and it found everything.