We are a startup, deploying an application that will require a monthly & yearly license fee from users - nothing too complicated. This is our first startup, and we've seen a range of opinions online on how to process payments. I'd be interested to hear how YC'ers have tackled this question!
We've created a free API and "lowest cost" processing model that is working well for what amounts to subscription fees in your case. coachfrits1-blog@yahoo.com