No real need for a script to do it either, beyond knowing where the last backup was. The --link-dest option in rsync takes care of all the symlinks that people used to use cp -R for. I started using that option at work to hang onto more builds without chewing up so much disk space, and it's worked well so far.

As far as the backup method and mailbox type, it depends on the backup program. For some reason my mindset of backup is still stuck in Windows land, where it's uncommon to see effective use of things like rsync and such. Instead, a ton of backup utilities there would do what I had talked about above, simply looking for files that changed, then throwing the entire contents out to tape or wherever. Time Machine on OS X works in a similar way, moving the entire file over to the backup if a bit inside of it changes.