Complete backups for the iPhone?

On a PC, I copy the whole operating system partition including
programs, and keep an extra backup copy of personal data. When
something goes very wrong... If possible, the most recently
changed personal data is copied out, then Windows is deleted and
replaced with the most recent known-good copy (unless there is
some good reason to regress farther), and then personal data is
replaced with the most recent stuff. That makes for a nearly
bulletproof computer here.

I would like to figure out how to do the same for the iPhone, or
at least learn whatever other possible backup schemes there might
be.

Using a jailbreak file manager (like iFunBox), apparently I have
access to most of the data on the iPhone, but I am inexperienced
with that and do not know how accurately it is able to move data
to and from the iPhone. Assuming it is accurate... The first step
might be to use a firmware restore as the base and figure out
which files are changed and added after a restore (and copy them).

References would be appreciated too.
Thanks.