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.