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Personally, I have a scheduled command which packs the data into a tar (no compression) and copies it to another of my servers (using SCP in linux).
I guess the ideal way to backup your stuff depends on what kind of site you run, how much data you have, etc.
If you have a database-heavy server, you could setup replication to a small server so it automatically replicates all data.
On my previous setup, the websites ran in a virtual machine which I could take an entire copy/clone of regularly and store it wherever appropriate. Not ideal if you don't know how to set that up, but it has the benefit of being able to restore the entire system (OS, files, etc) as is.
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