This means that when I open the preferences dialog (for example), the tool-tips for the dialog's buttons appear *behind* the dialog itself, and the same goes for pop-up menus! This makes inkscape pretty hard to use, to say the least :-).
I can't suggest anything but set "Dialogs on top: None" in preferences. This makes dialogs behave as regular windows. If this does not help, Inkscape can't really do anything about it. The real problem is with GTK implementation for OSX. Try upgrading your GTK and/or submitting a bug to the GTK developers.
(I must say that I have several other X11 applications on my Mac [OpenOffice, Gimp, XEphem and Scribus], and they don't have this problem).
Which version of Gimp? Have you tried the latest 2.1 series? I'd be interested to know how it behaves on OSX.