Google Checkout API
As you already read in the news Google launched a few days ago Google Checkout, its online payment service. Dubbed 'GBuy' may be an alternative to EBay's PayPal (already eBay restricted Google Checkout as payment method on its auction site). One big minus is that is available only for US (for the moment, I hope).
I won't comment here too much about this new service, features or fees but mention new API. New Google Checkout API allows you a deep and secure integration with web/desktop apps. They offer samples for ASP (IIS), PHP & Java, with full documentation for each of these languages. Here's a link to PHP sample.
Files with their functions available for integration into your custom application are not trivial, but easy to understand. Give it a try and see if they are ok for your needs.