Sniper223 notes a PC World article on a new kind of rootkit recently developed by researchers, which will be demoed at Black Hat in August. The rootkit runs in System Management Mode, a longtime feature of x86 architecture that allows for code to run in a locked part of memory. It is said to be harder to detect, potentially, than VM-based rootkits. The article notes that the technique is unlikely to lead to widespread expoitation: "Being divorced from the operating system makes the SMM rootkit stealthy, but it also means that hackers have to write this driver code expressly for the system they are attacking."
rdiff is one of a number of programs (cvs could also work for you) rdiff only copies over the changes and keeps logs of the changes, so roll-backs are possible for data recovery.