Factual error: Season 3, episode 49 (Not What It Looks Like). Breaking glass with sound is possible, but would not work as depicted in the episode. First, in order to break the glass, you have to force the glass to vibrate at its natural frequency - that is, the frequency at which it would vibrate if it were tapped. Each piece of glass has its own natural frequency, depending on a range of factors including size, chemical makeup, shape, hardness, and manufacturing methods. No single frequency would shatter all the glass in the store at the same time. Finally, in order to break the glass the piece has to be closed-ended. You can't shatter a plate of glass with sound (nowhere for the sound waves to resonate). Please see http://www.madsci.org/posts/archives/feb98/887203231.Ph.r.html
Factual error: Danny explains how the glass was broken using ultrasound waves to hit the glass at their resonant frequency. He explains it could be done using a mp3-file and a mp3-player. As mp3-players are designed for the human ear, the upper frequency limit is around 20 khz, far too low to produce a sound capable of shattering glass.
Revealing mistake: After Danny breaks the glass in the lab allegedly using sound waves, you can see in the shot immediately after the glass breaks, a thin green laser beam from roughly further top left to near bottom right. It's assumed this is what actually broke the glass.