BlanketJS is a fantastic code coverage tool that works well with QUnit. I've been using it for about a year now.
For larger projects, I also have QUnit and Blanket integrated with Grunt so I can run my tests, and check my code coverage thresholds from the command line, as well as CI solutions like TravisCI.
There was no existing Grunt plugin that fit my needs, so I wound up writing my own Grunt plugin. The plugin supports "enforcement" of a minimum threshold, or else the Grunt task fails.
I wrote a blog post with all the details here: http://www.geekdave.com/2013/07/20/code-coverage-enforcement-for-qunit-using-grunt-and-blanket/