The MySQL docs have some information about
keeping passwords secure.
I'm not sure they'll help you a huge lot, since
you're going to be using some sort of CGI script,
yes? Perhaps you could investigate some sort
of wrapper, yes--perhaps you could use a wrapper
like cgiwrap (isn't that it?) that runs the CGI
script as you. Which would mean that you could
make the file unreadable by users other than
yourself.
Another thing to think about here, just as a
reminder--since it sounds like you're dealing
with pretty sensitive, critical information--is
that MySQL doesn't "do" transactions. Which means
that errors can leave your data in a less-than-desirable
state. :) (An inconsistent state).
If transactions are important to you, check out
PostgreSQL or, if you have a lot of money :),
Oracle.
So, you've probably already thought about that,
but in case you haven't, I just wanted to warn
you. I have no problems w/ MySQL, because I think
it's definitely a great product... but just for a
particular purpose.
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