I used the Pipe Organ puzzle as part of a quest where the players had to investigate a cult temple located in a series of sunken caverns. After making it through most of the cult living space (dorms, dining hall, etc...) the players come upon a high-ceilinged underground chapel. Rows of pews on each side of the rectangular room, 15ft. tall pulpit at the front of the room. There is no apparent exit from the room except for the door through which the players entered.
The centerpiece of the chapel is a dusty old pipe organ with 50-100 pipes stretching up to the ceiling. Nestled in the center of the pipes, about 5 feet above the dual keyboards, is a stone statue of a winged beast (I used the image of a winged minotaur, because that was the avatar of the cult's demi-god).
There is a secret door on the wall behind and to the right of the organ, but the players have to play two specific chords on the organ to release the locking mechanism and open the door. If the players play any other keys, other than the designated chords, the stone statue (revealed eventually to be a supped up gargoyle) springs to life and tries to chew their faces off.
The only way to detect the proper keys is with a detect magic spell (I used this one to encourage our mage to cast detect magic more, as they were running in to all sorts of nasty magic traps w/out checking first). Once cast, the proper keys give off a faint conjuration aura (pressing them causes a missing gear in the door assembly to appear).
This one is also fun because if they fight the gargoyle, which the probably will end up doing, there's all kinds of cover to be had in the form of pews, pulpits, etc...
Variation: If players are having trouble figuring out what to do, you can place a music box on the corpse of the slain gargoyle that plays the two distinct chords. Playing them requires a performance skill check though.