A full answer: (Tested with r71)
To set a background color use:
renderer.setClearColor( 0xffffff ); // white background - replace ffffff with any hex color
If you want a transparent background you will have to enable alpha in your renderer first:
renderer = new THREE.WebGLRenderer( { alpha: true } ); // init like this
renderer.setClearColor( 0xffffff, 0 ); // second param is opacity, 0 => transparent
View the docs for more info.