I use synctoy to a nas (NSLU2 with 2 WD my books) and acronis to backup the system itself. I actually use acronis to backup every system in my house. The only issue I have right now is that I can't get the huge files onto the NSLU2 due to ext3 file size limitations.
My next move is to rebuild one of my older systems to the MS Home Server product. From what I've seen, that may be the perfect situation. It allows for backups of the data (with a pseudo raid provision) and the OS's. I'm sure, given that it's a MS product, that there will be challenges, but I've seen quite a few positive reviews.