I just found out that you can change the color of the mini-windows when Exposé is activated by using APE Manager from Unsanity. Specifically, the color of the mini-windows when you roll over them is the same color as the Background Fill Color choice in the ClearDock APE. It even uses the opacity setting. Nice!
Mac OS X Hints
http://hints.macworld.com/article.php?story=20031026161724347