Thunderbird 5 brings a custom chrome on Windows Vista/7 that uses translucent Aero decorations on toolbars and menubars. Here is how to restore solid backgrounds if you don't like it.

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Put the following into chrome\userChrome.css in your Thunderbird profile directory:

@namespace url("http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul");
window {
  background-color: -moz-dialog !important;
}

(Re-)start Thunderbird afterwards.

If you need more info on where the userChrome.css is supposed to be, cheat with the note on how to remove buttons in the message area.