I would never pain a 360 controller. I would either make it too glossy or I would have a run or since I would be all detail oriented I would want to paint all in the cracks the shit so it would probably not fit back together again.

This is what I would do if I wanted to change my controller colors:

Amazon.com: eForCity Shell for Microsoft Xbox 360 Wireless Controller , Red: Video Games

If you search Amazon they have all kinds of difference shells for around 10$ and then you don't have to worry about pain chipping off or it not fitting together right. And they have tons of colors and transparent ones and metallic ones. You can't do that with spray paint.

Just look at the options:
Amazon.com: 360 controller shell