I've got a 2006 tc, I need to know which wire is the ignition wire. I've got the iPod equipped HU if that changes anything. On the back of my head unit there are two gray wires. I'd really like to know which wire I need to use, I've got all of my speaker wires spliced and such, the remote wire is what I desperately need help on now. Any help would be greatly appreciated.

Read this thread, go to the third post and it has all the wire colors you would ever need(almost).
http://www.scionlife.com/forums/viewtopic.php?t=42276

There are four harnesses plugged into the back of the unit, actually, five, but one is unused. I assumed the speaker harness was the one with the eight wires coming out... which of the other three harnesses has the ignition wire?

It should be in the 8 pin harness, that harness will have Constant 12 v, switched 12v, illumination, Ground, Front left positive and negative and front right positive negative.