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Both are good toolkits that have their advantages and disadvantages.
One difference is the implementation language. Qt is in C++, and GTK+ is in C. However GTK+ has bindings for many, many other languages (perl, python, C++, .NET, etc) so it's not a huge issue.
An Advantage of Qt is that it offers a bit broader range of functionality built in (xml, database access, network programming, openGL, etc). GTK+ has basically all of these things within its orbit (e.g. libxml2, librsvg, libsoup, libgda, etc), but they're not as much of a single coherent package as Qt is.
My personal recommendation is to use gtkmm, the C++ bindings for GTK+. It offers a more comfortable object-oriented language to program in, and it provides nearly the same native performance as using GTK+ from C. (Disclaimer: I contribute to gtkmm).
Qt 5.0 has won the war. I'm not a huge fan of C++ (I prefer plain old C), but I must admit that the Qt framework is amazing. Try to write a GUI program with GTK that runs on OSX, Linux, Windows (and soon iOS and Android) with native look-and-feel... Good luck !