I've never had a problem with GTK apps in Ice - QT apps look like crap without KDE, though, so I played around with ~/.qt/qtrc in the [Palette] section. As far as GTK, it'd mostly be ~/.gtkrc. Not sure about Python apps - don't they usually use a GTK or QT lib for the UI? I customize nedit (motif) through ~/.Xdefaults. Of course, each app has its own internal configuration for a lot of things. As far as *what* to put in them, I've never found any decent documentation on the gtk and qt rcs so I just type in random crap and see what happens. Sorry I can't be more specific but it might be something to look into until someone else posts.
Oh, and I don't use Gnome or KDE so I don't worry about screwing them up - for all I know changes you make in Ice would make them look funny back in Gnome or KDE.
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