In my experience, having made both PyGTK and PyQT apps, there is little difference on the underlying programming side of things. PyQT seems more consistent across different flavors of Linux, where GTK is constantly changing and breaking on older distributions.
PyQT has QTCreator, which is a great GUI designer. PyGTK has Glade3, which is getting better, but not as good. Until recently Glade was a bad joke. If you need to draw GUIs in an editor, PyQT is probably the better choice. Otherwise, I'd go with PyGTK for coding because the online PyGTK documentation is excellent.
One bizarre thing I've found is PyQT has poor support for dynamic menu item callbacks. Maybe I just didnt use it right, but PyGTK is a bit more flexible in comparison.
It's a tough choice, really. But if you design your application right, the interface should be irrelevant; you could design your app with multiple interfaces...