The episode of Star Trek: The Next Generation called "Phantasms" clearly references frequency medicine.

Pay attention to what Data does to get rid of the parasitic organism taking over the ship. He emits a sound from his mouth at a specific frequency - it even sounds like a square wave.

http://www.youtube.com/watch?v=zBmXYlri5dk


Don't feel like watching the whole episode?
http://memory-alpha.org/wiki/Phantasms_%28episode%29


"Data makes the shrieking sound, which immobilizes them. Data wakes up and says he knows how to get rid of the parasites. By reconfiguring his brain to emit an interphasic pulse, the creatures are killed. "

Other interesting tidbit.
"Crusher then discovers an interphasic organism on the wound - and on several other crew members, including herself, Captain Picard, Commander Riker, and the entire medical staff. Crusher determines that the Enterprise is infested with the creatures, which are feeding on the cellular peptides of the crew's cells. Everyone has a creature attached to them somewhere, and they can only be seen in a certain light.." Is this last bit a reference to Royal Rife's famous microscope?