There are alternatives to using FlyNap. My Biology teacher and I experimented with them when the FlyNap shipment did not come in.

Alternative one: Freeze the flies for a short period of time, in order to calm them down enough that they can be transferred to a petri dish for sexing, etc.

Result: Half of the flies die. The other half are knocked cold (heh, heh) but reawaken as soon as you have the petri dish closed and have no way of getting them back into the habitat vial without freezing them (killing most of them) again.

Alternative two: Oxygen deprivation.

This was my idea. We placed alka-seltzer in a beaker with water, and routed a tube into the habitat. This didn't kill quite so many, and they seemed to be rather securely unconscious. We opened the top, started to shake them into the dish, and by the time the oxygen had hit them half were already in the air. It was a mess... and five lab groups were doing it before we realized what was happening. We spent a few minutes trying to catch those that we could (futile), and gave up.

Alternative three: Use rubbing alcohol in place of FlyNap. Deposit a drop into each habitat vial.

This kills all of the flies.

At this point, we decided that there were no other alternatives, and postponed the lab until FlyNap (and more drosophila) could be secured. We did nothing for nearly a week. Mission successful.