I was able to change the taskbar color like this:
1) Enable custom themes by running VistaGlazz 2.0 or other theme patching tool: http://www.codegazer.com/2009/11/11/vistaglazz2/
2) Make a copy of the aero theme by duplicating the C:\Windows\Resources\Themes\Aero
folder. You need to rename the aero.msstyles file to the name of your custom theme.
3) Duplicate the C:\Windows\Resources\Themes\aero.theme
file. Edit it with notepad to point to the new theme folder
4) In the new msstyles file, edit the IMAGE resource with number 845. It is a PNG image for the taskbar when it's at the bottom. There are other images for taskbar on the left, right, or top. The image is 3 pixels high. The top 2 pixels form the top border and the 3rd pixel is used to fill the rest of the taskbar. Change that pixel to whatever color you want. I did this primarily to remove the transparency because I wanted an opaque taskbar. You can also add more pixels at the bottom to create a gradient. All the pixels except the first 2 will be stretched to fill the height of the taskbar.
5) From the theme settings activate your new theme.