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You can take payments online in a number of ways. The first is PayPal - this an inexpensive way to start taking payments quickly, especially if you don't have a merchant account. With PayPal, your visitors can pay you with a credit card or by sending a payment from their checking account (echeck). PayPal provides a shopping cart and many other free services that are helpful to sites that are starting out. They charge 2.9% +$.30 per transaction and have no start-up fees. The downsides are that PayPal is not a very customizable solution, and it can have a “start-up” feel. However, this is changing and many mainstream sites are now accepting PayPal as more and more people have PayPal accounts. PayPal is inexpensive both because there are no merchant account of payment gateway fees, but also because PayPal provides a very easy way to integrate their shopping cart into your site, which reduces development time.

A similar solution just for non-profits is Network for Good, which allows you to accept credit card donations on your site. They charge 3% of each transaction.

Another inexpensive option is a free solution called Mal's e-commerce. Mal's is a shopping cart system that is remotely hosted. With the free version, you can accept PayPal, offline payments like checks, and credit cards if you have your own way to charge them already. It will store the numbers for you to run offline. For $6 a month you can upgrade your cart so it can integrate with a number of popular payment gateways like Authorize.net. There are other fees associated with payment gateways and merchant accounts that you would also be responsible for. Here is a comparison of PayPal vs. Mal's.

Finally, there is the option of creating a full e-commerce solution. This involves many different components - a merchant account from a bank, a payment gateway service that allows you to accept payments into your merchant account from your website (this is often bundled with the merchant account), a shopping cart or payment script that integrates with your payment gateway, and certain elements of the server environment like having an SSL certificate and a static IP. There are some shopping carts that are available as pre-packaged scripts such as Magento that can be customized for your situation, or a custom payment script can be developed that exactly matches your needs. Full e-commerce is much more expensive and time-consuming to develop than PayPal or Mal's, but it can be integrated into your site for a truly seamless payment experience. It can also save you money in the long run if you are doing a high volume of sales.