It probably depends on what you want to do. I would recommend Qt, because it's more than GUI, it has nice Python bindings (so does Gtk), and GUI libraries themselves are (subjectively speaking) more pleasant then Gtk.
Gtk is on the other hand more common in linux world, so you can probably get more help on the web. Reason for widespread of Gtk probably has more to do with Gnome and Ubuntu, rather then technical merits, but if you want you software to blend nicely with those two, you'll achieve that more easily with Gtk.
