some of this has already been said....
IE8 Tabs are not skinnable.
The background area on the favorites menu in explorer is not skinnable (see #1), so when you try to skin the favorites menu, it looks like crap. I've noticed that many skinners just leave this section white because of this issue.
The text on the buttons for the Command Bar is not changable (see #2). I'd love to at least be able to lose the shadow on the text.
The text color on the folders menu button needs to be changable (see #3).
I would like to have ALL the states for the start button capable of being animated, not just the mouseover.
A seperate image for the start button for the vertical taskbar (see #4), so we can center it or not, depending on the blind.
The user picture background isnt skinnable (see #5), I usually just get rid of it because it will not match.
The flashing button for the vertical taskbar needs a seperate image.
The text color settings for the pressed, disabled and mouseover states on the Toolbar Style Menubar Button are mixed up in SKS6 and SKS7.
Color Burn and Color Dodge would be nice to have in the blending options for layers.
It would be nice to be able to move the Start Menu Log Off Buttons independantly from the Search Bar on the Start Menu.
The Search Icon in the Start Menu Search Bar will not stay centered in the search bar if the bottom section of the Start Menu is too tall (see #6).