A couple services that come to mind:

http://spreedly.com/ http://zuora.com/

Zuora is mucho $$$ though, and Spreedly has a ways to go before it's a full-featured solution. Their current focus I believe is on being solid with regards to ordinary subscriptions first and expanding from there.

Unfortunately, for most of the projects I've done, there are too many types of transactions, extra costs, etc. so I've had to roll my own. I've built a somewhat reusable app for this now, so it's a time saver now, but it was a huge time waster earlier on.