At this point, I think we all have our own favorite PhET sims. You might be able to start a fight among physics teachers by proclaiming your favorite is the best PhET sim of them all. But honestly, what's not to love about John Travoltage?
When we get to wave optics, we use the light module to develop interference pattern mathematics. As we begin the study of mechanical waves, we explore representations in the water wave and sound modules.
Water Waves in an Electric Sink (Google Docs copy link)
Students begin with examining a pulse with the sim's various view modes. Then it's on to continuous wave trains while varying frequency and amplitude.
High Quiet Low Loud (Google Docs copy link)
Originally developed for use with Pasco's Waveport DataStudio software, this activity has been redesigned around Wave Interference's sound module. This time, the manipulation of amplitude and frequency is accompanied with audio feedback. The sim's "Particle View" feature shows that matter doesn't move much even as a wave propagates across greater distances. Diving deeper, we notice that our sound waves appear to be moving through a solid in the sim.
I couple these with The Mechanical Universe - Episode 18: Waves and Paul Hewitt's Conceptual Physics Alive! Vibrations and Sound I and Vibrations and Sound II to round out much of the introduction to waves.
In any case, I'm sure there's even more to PhET's Wave Interference than I am leveraging. So much groovy wavy goodness!