I use Qt for all my window needs, even if my app is not going to be cross platform. I highly recommend it. (note: if you use Qt, I suggest you go to qt-project.org (not qt.digia.com), because that's where the open source Qt community lives (qt.digia.com focuses on commercial services)).
However, I've never used it for a game. I've used it for tools and other programs. But when it comes to an actual game, I typically code a custom OpenGL GUI system.
In short, if I want a "native look and feel" to a window, I use Qt. If I want a GUI for a game, I write it myself, so I don't have experience with other OpenGL/D3D GUI systems to recommend.