Call a few other stores. My wife had her heart set on a 16" Trek 3700 in Purple. The LBS said "sorry, Trek is out of purple, I'll get my Trek rep on the horn and see what we can do" so we milled around the store and he came out and said "Trek sold out of the purple ones at the factory, we can back order one but they aren't even made yet so it could be a few weeks, if you want you can pay for it now and we'll call you to pick it up when it's in".
We said "uhh we'll think about it."
Went to another trek dealer, they had many purple 3700's in stock in many sizes. We asked the manager there about the "shortage" and he said "what are you talking about? we've had no problem getting purple ones..."