I think the easiest/simplest way is to just use rsync for the backup (that can be automated easily). I know it isn't good practise to run a backup on a live system since files can change during the backup, but if nothing is running at the time, it shouldn't cause an issue.

I have myself used rsync to clone one N900 to another and it didn't have any issues, though I haven't incorporated it into a regular backup strategy.

The only thing you have to watch out for is if you are restoring to a clean N900 you need to install the kernel (or a kernel if you have multiple installed) that was installed on the device when the backup was run.