Maybe a sector-by-sector backup allowing for a bare-metal restore would be the best option here? There are plenty of these for Linux. I've used two of them in the past, but I have forgotten what they are called. I began with Ghost4Linux but when researching it I found something else that was easier and simpler - there was a Live CD that I booted from, did the backup (to a network share in my case but there were many other options), and restored in the same way. In the event of a disaster, you then just restore the backup. It takes a long time, and I don't recall if restoring individual files or directories was possible. And like I say, I don't remember what it was called
There's also an excellent commercial product from R1Soft that does a full sector by sector backup and allows you to do a bare metal restore. The problem is that it is expensive, and you need a client running on the machine you are backing up, and the server running on the machine you are backing up to (in a simple case).
Some hosting companies and some online backup service companies offer an R1Soft backup service. They tend to be very expensive because the product offers *continuous* backup with full MySQL database support (as an option).
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