@stalka - That's a good point, but it doesn't actually work I am afraid.
1. Whilst changing the windows background colour will cause the sys tray icons 
to update their background, they will still not match the actual theme 
("Ambiance" has a gradient in the panels, and you can't match that with a 
simple colour change).
2. One's windows backgrounds will now be dark unreadable unless you change the 
text colour, and white text on a dark background may not be what one wants.  So 
unless your panels happen to match your windows background, one'd still be 
goosed.  This is why "Cleanlooks" appears to work.  The panels and the window 
background happen to match, but the problem is not actually fixed.

One could switch to "Radiance" where the problem is less obvious I
guess.

There was a "sort of" similar issue with Skype and menus,
Options/General/Choose Style/"Desktop Settings"/Apply seems to fix that.
I am wondering if there is a sort-of similar switch for Wine?  I've dug
around in gconf, but can't see anything obvious.

@Marcus Carlson - it might mask it I guess (I doubt you would get the
gradients).  How does one access the background setting for panels?  I
don't see it with the Theme customisation GUI which is the only way I
know how to set things like that.

@Tim Kosse - Thanks for the heads-up.  I am only affected by the Wine
issue, but not being a dev I am not sure if Wine is dependent on
wxWidgets.  Nor do I want to risk installing wxWidgets 2.9 in case I
futz my system up!

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Notification area icon wrongly rendered/uses bg_color as a background (multiple 
apps)
https://bugs.launchpad.net/bugs/403135
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