I've managed to work out how to alter just about everything else - the titlebar, menus, buttons, etc.

But most X applications still have the same drab grey background. The menu bars in Firefox are grey, Grip's background is grey, Jpilot is grey... everything is grey!

Is it possible to change to a more interesting color, and if so, how?

install fvwm themes and copy one theme settings that you like a little bit in your ~/.fvwm/themes/personal/ and hack it.

As far as I understand you have configured the Windowmanager (FVWM) to you liking. The contents of the windows however are at the complete responibility of the contained application, respective the used toolkit. In the worst case you have to figure out how to change each applications properties on its own.
That's what KDE and GNOME are for. All KDE and GNOME programs use their desktop environments settings, so if you for instance change the background color in the KDE Control center, all (and only) KDE applications will adapt to it.
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Rud