I implemented some 3D transformation and rotation tools today, including a pixel perfect click-to-select, using a specialized frame buffer that holds object indices. To streamline my own editing I implemented a similar system to Blender's in maniuplating translation and rotation, using keyboard hotkeys like G and R and selecting axes with X,Y and Z keys and orthographic axis views.
The initial reason I went into all of this is planning to implement a spline based track editor, but that requires manipulating spline points in 3D space, and this is the basis for that.