To us, the Home button light looks just like a reflection of the background. Or maybe it's just a cosmetic difference so you can say, "hey guys, I bought an 80GB PS3 and here's my red light Sixaxis to prove it!"
Update: According to Patrick Seybold on the official PlayStation.Blog, "Just want to clarify for those wondering why the PS Button on the controller is red. That is what happens when you charge the ... 'debug' controller. It is not a sign or indication of a new/different controller with the 80GB model."
[Via Engadget, PS3 Fanboy; thanks, BulletToothTony]