I pulled my center stack apart so I could replace a cruise module and replace a burned out light in the climate control. I found attached to the stereo harness, 2 extra plugs. They were not plugged into anything. One is a flat, black connector with a brown and white wire. The other is a square shaped connector with brown, black, blue, and red wires. What are these for?

 

Pics would help

 

There:

 

It could be for some features of the sound system your car is lacking. I'm not sure if there is a "Premium" and "Regular" Bose system, or what the difference could be among them, but I do know that some cars have CD changers in the trunk and others don't. The guys at the Audio and Electronics sub forum should know.

 

Even if it were for a CD changer, that would be in the trunk and there is not a spot in the head unit for the 2 plugs to go into....

 

I misread your post; I thought those plugs came from the back of your HU.
EDIT: The small one looks like the one that goes to the Ash tray light.

 

I can't see the other one completely, but the only thing that comes to mind is the cigarette lighter, unless yours is working.

 

The ash tray light is a skinnier one that is white.