Collecting payments online is something that we all hope to do with our online businesses; it's important to use reputable, reliable and well known providers as your customers are putting their trust in you.
Here are the tools I use for payment integration and automated processing...
Well established and integrate easily with most popular shopping carts
Stripe has been providing payment processing solutions to Internet businesses for as long as I can remember. They are well established and integrate easily with most popular shopping carts. So if you are having trouble securing a merchant account with your own local bank or you need a reliable payment gateway, I would recommend giving Stripe a try.
A great and complete payment processing solution
I used to tell people PayPal was a great payment processing solution for when you were just getting started, but their systems and services have expanded and grown so much over the years that they can now handle the payment processing needs of larger businesses acting as your shopping cart, payment gateway, and your merchant account.
The only time I would not recommend PayPal as your primary payment system is if you are in a business that may be considered higher risk (i.e. business opportunity, dating, etc.) and generates slightly higher than usual refunds. PayPal has been known to be a little trigger happy with freezing accounts and can be more difficult to deal with in these cases.