I still can't find a way of changing the default white color of applications window backgrounds. It does hurt my eyes and I used to adjust it so easily up to 10.04.
There was this post: How to change the background colour of a window?, explaining how to tweak some things, but they don't affect the white background.
Also another sufferer tried to ask the question How to change the window color (default: white)? but it was closed! Please help.
The problem you are facing is due to the change to gnome (and gtk) 3 , so there are not yet as many themes available.
For advice on how to manually customize your theme See How do I make a Theme from scratch for Unity?
You can try themes from
Over time more an more people will likely contribute themes to gnome.look
http://gnome-look.org/index.php?xcontentmode=167
Sometimes the themes (from gnome look) work and sometimes they do not (I do not play with them much)
