Placing the masterpassword

Hi all I got a little question about a good application design in PHP. If I use a mysql connection for example, I have to store my mysql-password somewhere in the code. If it's just in the mysql-class, that's not that good, because if somebody changes the functionality, he'd see it. I also can't store it in a text file. Until now, I just created a password class where all the passwords are described and i can get them by a get-function. Where are passwords stored in the big applications? There has to be at least one big masterpassword somewhere - how can I store it safely? How is this problem solved in big systems in production? Thanks for help ;) Regs, Flo.