I am posting this so that my process may either inspire or save someone from hours of work.
On my system I use a 120GB SSD for OS and Apps, data and all other items are stored on secondary hard disk. I use Carbon Copy Cloner to make backups of my SSD onto an inexpensive USB external HDD.
Yesterday my Mac locked up and when rebooted would not load, took SSD out and could not mount it on my MBP or MacMini, couldn't mount it on Windows7 to even reformat it. Its under warranty so no beg deal there, I have a spare HDD and restored my backup clone to that drive and I was up and running except for a few small things that need to be done.
What could have been hours of down time was mitigated by keep an up to date clone of the boot drive. It only takes about 20 minutes to clone your boot drive. I do it when I go to lunch and its done.
related link - free software