Hi there,
That's a great question - graded courses will always trump MOOCs when it comes to building alternative transcripts if you have flags. Say, for example, you didn't too well in Calc. If that's something you're trying to remedy, you need a graded course to show the adcom, "look, I know I didn't too hot the first go around, but I retook it and rocked it - so don't worry, I have calc covered!"
However, MOOCs are beginning to gain momentum and gain real credibility. They're useful for folks who are trying to demonstrate passion or show they're committed to a career change of some fashion (among other things). So that way, an adcom can see that you're putting time and effort behind the words you're saying.
They're all tools, and depending on the job, you're going to use a different tool. Let me know if you have any questions!
Bhavik