Security Question - not specific to informix

Greetings, I'm faced with a project that deals with accessing databases by way of ini or config files. Basically the apps/scripts are sourcing files to gain passwords. Some of which are in plaintext. These files can be on windows or unix boxes. The programs from .Net or Power Builder to VBS and shell scripts. Can be interactive or non interactive and are batch type in nature and can run from cron and or windows scheduler. Guess my question is how are others doing this and or not doing this? Industry Best Practices? etc... Single signon, encrypting/decrypting tool, etc... Also, if you know of any security companies that deal with this. I've already talked with RSA Security and waiting info from HP. Any insight into what others are doing would be greatly appreciated. Thanks