What causes the retina Macbook Pro HDMI-DVI output to cut out on occasion?
Try disabling Automatic Graphics Switching in the System Preferences-Energy Saver.  This may be working for me, though I haven't figured out how to reproduce the 1-2 second blanking, so only time will tell.  

I'm running 10.8.2 on a new rMBP and have the same issue - The external display goes blank for 1-2 seconds when connected to a 1680 x 1050 display via the HDMI connector and the rMBP is closed and in a stand. There is no movement of the rMBP, the HDMI cable or monitor when this happens.

I have not experienced the same momentary blanking of the rMBP's display when using only the native display.

It doesn't happen often (2-3 times per day) so it's more of an irritation that I don't expect from a nearly $3,000 piece of hardware.