- Environment variables
- Per-user config files
- Command-line switches
- Prompt the user at run-time (ie. STDIN)
Take your pick but bear in mind that most of these have security concerns depending on who has access to what.
Also be aware that any coder working on a script can have it output any data from the script in any form (save to a file, email it, FTP it, whatever) so you have to trust the coder at some level.
Addendum: Also consider the related FAQ