I can't believe I still recognise that.

The Nikons that support CLS (Nikon TTL) use preflashes to control the other flashes. If you use the onboard flash it's visible light, an SU-800 (control only, no flash) is all infrared, not sure on the SB-800/900. You do get a bit of light from the onboard flash that will contribute to the exposure, but for most situations this won't cause an issue.

Also apparently the Pocket Wizards support all of the Canon TTL flash features (though not Nikon yet). But they cost......