Take a look at Customizing UI Branding.
Something else you can do is manually alter the colors in some key files. (You won't find this in the documentation.) Here is a picture of what my test system looks like and the files I changed to get there. (This is for 10.2)
codebase\netmarkets\themes\windchill\Header\
- back_tile.png
- left_gradient.png
- slash.png
codebase\netmarkets\themes\windchill\navigator\
- navbackground.png
- navbackground_over.png
codebase\netmarkets\themes\windchill\panel\
- BG_stripe.png
- BG_stripe_gradient.png
- BG_stripe_tile.png