There are many possibilities for conducting transactions over the web, from simple and cheap to complicated and expensive.

PayPal
The cheapest/easiest is PayPal - this is 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 an "amateur" feel.

PayPal is inexpensive both because there are no merchant account or payment gateway fees, but also because PayPal provides a very easy way to integrate their shopping cart into your site, which reduces development time. To implement it, just sign up with PayPal, and click on Merchant Tools, and then on Make Shopping Cart Buttons to get started. You will input your options for each product and it will produce a snippet of HTML code which you put in your page where you want the "Add to Cart" button to be.

A word of warning: Paypal has been known to seize merchant funds under the guise of the need to make an "investigation" concerning a transaction. They have been known to hold these funds for up to 6 months. It is for this very reason why we no longer use Paypal as an alternative payment system. Use them at your own risk.

Non-profit Payment Solutions
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. There are other services like this (try a Google search), but this is the most popular.

Mal's E-commerce Cart
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 securely 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. In this case you would also be responsible for merchant account and payment gateway fees.

Fully featured shopping carts
Finally, there is the option of creating a full e-commerce solution. This involves several 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 sometimes bundled with the merchant account as a complete package), 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 the fully featured X-Cart 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.

Merchant Accounts
There are many merchant account to choose from, often including your local bank. E-onlinedata is the merchant account provider we have chosen to work with.We did several months of research and determined that e-onlinedata was the company that had the best balance of low fees, solid customer service, and experience serving online merchants. We have published a testimonial of a merchant that chose E-onlinedata. You can read it here.