Our program was initially affected by Wine bug 2398, i.e. the bug that causes the OpenGL window to occupy the whole application window.
I forgot to mention this in my first mail, but Roderick Colenbrandner is working on a patch that is supposed to fix the child window issue at its root. Basically it creatses an X11 child window for the opengl target, thus the gl rendering goes where it is supposed to go. It is only targetet at fixing opengl apps for now, but it should be easilly extensible to fix d3d apps too.
The patch works in general, but it has some nasty issues left. Moving windows or gl rendering to grandchildren, or if the X11 child window is supposed to be covered by another window.