I think that there are a few different kinds of Mac indie developers. Those who don't want to have to deal with customer databases and payment processing might as well just use the Mac App Store as the distribution mechanism. Then there are the people who want to be able to sell directly to customers, but want a full-service company to handle the processing issues. FastSpring is great for that. But if you want more control over your purchasing experience, and you can set up some scripts on your server to manage license generation and charge cards, then Stripe is a great way to go. (And also, possibly, PayPal for those prefer that option.)
I’m pretty happy with PayPal Website Payments Pro for payments and E-junkie for the shopping cart, but if I were going to make a change it would probably be to Stripe. (FastSpring looks nice but overly expensive.) Stripe’s fees are higher than PayPal’s volume rate. PayPal adds a few fees, e.g. for the Pro API and for International transactions, but Stripe charges fees for refunds. Overall, my guess is that PayPal is cheaper, but not by a lot. Stripe sounds easier to use, but that’s balanced by the fact that I’ve successfully used PayPal for many years with essentially no problems. It would be nice if E-junkie integrated support for Stripe the way it has for Google Checkout and other processors.
Update (2012-10-24): Dan Wood:
This is a followup to that, describing what we did to build our online store, and what decisions came into play for its user experience.