(not sure where to post this since there was no reply over at the APM Forum)
after balancing my props I used the new Motor Test function in Mission Planner (1.3.5) to detect vibrations resulting from the combination of motors and props. Therefore, I hard-mounted the copter on a table and tested different throttle values. While doing so I listened to the resulting noise and tried to feel the difference in vibration. It works quite ok but is pretty analog and subjective.
To make this more efficient and more digital, it would be perfect:
This would allow for a much more in depth analysis of the causes of vibrations even before the first test flights.