In current version of gnome, there is no tools for setting up background color of window, it's background setting only change desktop's background.
I really don't like white background, I want the background gray, so I setup some applications's background manually, but some application do not have background color setting(e.g. some versions of Eclipse), and it's not a good way to do that, so I spent little time on it.
First I tried some themes, some of them has gray background, while I don't like there colors setting, so what I need to do is to modify some themes to fit my requirement.
In gnome's theme setting -> Theme Details, you can choose different setting of Controls, window Border or Icons, window's background belongs to Controls, I picked up !LighthouseBlue as a base setting.
The themes file are under /usr/share/themes, I only modified gtk-2.0/gtkrc
bg[NORMAL] = "#D0D0D0" //background color of window
base[NORMAL] = "#CCCCC0" //background color or controls
That make me quite happy. I didn't find good tool for editing theme, there is a definition of the values:
http://developer.gnome.org/doc/API/gtk/gtk-resource-files.html