On Thursday a long line at least 60-custumers long waited outside Apple’s clear, cube-shaped retail store on Fifth Avenue in New York City. Keep in mind that this store is open 24-hours a day, so a queue outside the store gives a point of reference.

An Apple greeter at the Fifth Avenue store confirmed that a line of people had started to grow outside the store at approximately 2:00 A.M. on Thursday morning. The reason? The customers were waiting for a new shipment of iPhones to arrive at the store. By 4:00 P.M. after the phones arrived and all of them had been sold, the line was gone. Apparently, the shortages of the iPhone and the long queues have become commonplace in the past few months whenever a new shipment of the iPhone is due to arrive.

Some Apple retail stores have reported difficulty in keeping the iPhones in stock, although the phone has been available in the U.S. for almost a year. This shortage has not been helped by the fact that Apple is due to release its new 3G iPhone on June 9th. Apple has apparently confirmed that the online store in the U.S. and the U.K. have been without any iPhones to sell for at least two weeks; they may still be available online in Germany, France, Ireland and Austria.

It is possible the coming launch of the 3G iPhone is contributing to the shortage of the original iPhone, and perhaps Apple is intentionally reducing its production of the older iPhone in order to phase it out as the 3G comes onto the market.  Whatever the reason is, there aren’t any retailers or manufacturers who wouldn’t like to be in this position where demand far exceeds capacity.