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Personally this is what I do.
I have an old Kindle 1 that doesn't even function anymore but I've kept its serial number registered to my Amazon Account since it was never up-datable past the firmware where the DeDRM script wouldn't work. Kindle 4 PC books would work for this also. I've kept the K1 around because I worry about Amazon someday forcing updates to Kindle 4 PC which might knock out the ability to remove DRM.
Every book I buy I go to Amazon and click transfer via computer and select that old Kindle as the machine I want the book DRMd for. Amazon sends a file to my computer and I immediately put that into Calibre. Calibre removes the DRM and also renames the file and saves it under a folder for the Author. I delete the original DRMd file from my computer download file then - no need to keep it around since the K1 it is DRMd to doesn't even work.
Then I click send to eReader on Calibre for my K3.
My computer gets backed up nightly to an external hard drive so I get a back-up of my Calibre there in case my laptop hard drive fails. Then I also have an online back-up service which gives me a 3rd copy out of my house.
So for my books I have
Amazon Cloud (or other retailers)
Calibre on my laptop
Calibre folders on my External Hard Drive
Calibre folders in my Online Back-up Service
and whatever books happen to be on my Kindle (all un-DRMd Mobi Files)
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