Amazon Flexible Payments (
http://aws.amazon.com/fps/)
Facilitate transactions between a buyer and a third party seller, take a cut of the transaction, and have control over who pays the transaction processing fees
This is the payment system used by KickStarter...supporters pay through the site, and when it reaches a certain threshold, KickStarter initiates payment to the project owner, keeping a percentage. Note that the money goes directly from the supporter to the project owner (and 5% to KickStarter) and not all into KickStarter's account first.
I think the eBay approach is good if you want to accept more payment methods, such as money orders and checks. This model ensures that you can always bill a seller's credit card even when the transaction takes place outside of your payment system.