Depends on which platform you are running on (Windows/Linux/Mac/...?)
As a platform independent way, I use a personal subversion server. All the valuables are there, so if I lose one of the machines, a simple 'svn checkout' will take things back. This takes some initial work, though, and requires discipline. It might not be for you?
As a second backup for the non-svn stuff, I use Time Machine, which is built-in to OS X. Simply great. :)
