It matters a whole lot what sort of payments you need to take. Is your payment model a sale (one-time transaction) or recurring billing?
If you're going to take credit cards and/or do recurring billing:
I've built two recurring billing payment systems (braintree and paypal express checkout) and maintained a third (paypal payflow pro gateway) and am most impressed with braintree's api thus far. http://braintreepaymentsolutions.com/ My braintree-based system hasn't gone live yet, so I can't say anything about long-term service, but their api was far more sane than the other two. That said, when we added express checkout to the payflow pro gateway, purchase rates increased substantially.
There are monthly minimums with braintree and a good bit of paperwork, but being able to directly take credit cards might add some degree of "seriousness" in the consumer's eyes.
If you're rolling on rails, you might want to check out http://railskits.com/saas/ (although I have no personal experience with them) and http://www.activemerchant.org/ (a payment library extracted from shopify).
If you're just doing one-time sales, you have a lot more options and the accounting is a heck of a lot easier.