If you were to create a skin that applied had a transparent property (the color "Magic Pink" RGB(255,0,255)) in the areas you desired, you should be able to achieve that effect (This would require some knowledge of Skin Studio, however). I am currently unaware of any available skins offering this feature.
WindowFX does offer this feature, however. You are able to make your windows any amount transparent, even fully transparent, as you request. Use "Transparency (Application)" and add the applications you want set to transparent (explorer.exe for folder windows).
-Mike
[Stardock support]