It's easier than ever to do this yourself now with PayPal, but there are still providers out there that offer payment solutions. I have used RegNow in the past (now MyCommerce:
http://www.mycommerce.com/regnow[
^]). I'm not sure if they offer a download (there's a bunch of solutions they offer that you'd need to research yourself), but they still offer a payment collection/registration service that will send you cheques.
Of course, if it's a Windows 8 application you can channel through Windows Store (similarly for Android and Apple).
Good luck!