Modify the transform filter to allow single-axis-at-a-time transformations
In some modeling software, when you are in transform mode (ie the transform filter) you can select a particular axis to translate/rotate about by pressing 'x', 'y', or 'z' before performing the operation. It is very hard to position an object in 3d without that ability. Maybe by clicking the "balls" at the end of the transform axes with different buttons you could specify that functionality.
This has somewhat been implemented. in the GUI, the X, Y and Z keys do work, allowing a user to rotate around the X, Y and Z axis.