Like Chris has already stated, there are legal ramifications to take into consideration. The major payment gateways put a lot of time and money into making sure that there servers are PCI Compliant in order to process transactions.
If you want to process the cards manually, you will end up having to put the same time and money into your servers PCI Compliance. an Alternative would be to capture the customers phone number, and call them to process the order over the phone, this way there is no need to store the credit card number.