Someone I know here at Harvard does work where she has to Kill Mice For Science. Apparently she had to kill another ten the other day. Before coming to Harvard, she would just break their necks. Now, she still breaks their necks, but apparently Harvard rules are such that she has to anesthetize them first. Interestingly, however, she says the rules do not permit her to just anesthetize them all the way to death. Instead: sleep, crunch. The only other permissible way is to kill them is by asphyxiation: you put them in a canister that pumps in CO2, so all they can breathe in is what they are supposed to be breathing out. She says she's done this before but won't anymore because she regards it as not unequivocally humane.
My own preferences, just in case I die and am reincarnated as a mouse in a lab (which, karmically speaking, I can't claim would be undeserved): anesthetize to death, anesthetize and broken neck, broken neck, trapped in a glass container with the wrong kind of air.