One of the key parts of security would be not describing it in detail on a public forum, so I wouldn't expect many people to give specifics on their procedures.
Some general advice:
- Always use SSL. You can get a cheap cert from places like GoDaddy.
- Always encrypt sensitive data. PGP, GnuPG, etc.
- Consider splitting the credit card number between two different places. Retrieve, rejoin & decrypt later. I believe some shopping carts already do this, by putting most of the # in a DB, then mailing the rest.
- Delete everything that's sensitive from the server ASAP.
- Familiarize yourself with all areas of security for any databases & languages you're using, or pay a pro to make sure it's done right.
- If you're using a third-party script, always make sure it's up to date. The more popular the script is, the more important this step is.
- Secure your home/work PC where the info is retrieved.