I have found it to be the most effecctive way to kill/stun a mouse, but if you are uneasy about using the "table method," some have mentioned using a pencil instead. I have never used the method, myself, so it is possible I have this wrong. However, I believe that you hold the mouse by the tail, then pin its head down with a pencil (or other similar object) just behind the base of the skull. Then, swiftly give a small jerk on the tail, and the spinal column is dislocated from the head, killing the mouse quickly.
I have heard that it takes a bit of trial and error to perfect this method, and some have inadvertantly pulled the mouse's head off in the process. Even so, I understand it to be very effective, when done correctly.
As an aside, you might find the following information interesting concerning the humaneness of the "whacking" method I use:
"A blow to the head can be a humane method of euthanasia for . . .animals with thin craniums, . . .if a single sharp blow delivered to the central skull bones with sufficient force can produce immediate depression of the central nervous system and destruction of brain tissue."
Under the heading of "Euthanasia by a blow to the head" in the Report of the AVMA Panel on Euthanasia, p. 681
Just a thought ...