My LBS gets your general frame size figured out, then adjusts the seat for you prior to a test ride. hey watch you ride, ask what you thought, and make suggestions. During the free fitting with purchase (which includes some measurements with a giant protractor and using a plumb-bob on your knee) they swap out what you need.

On my Trek 60cm, they swapped out for a shorter stem and slid the hoods back a bit. For my new 58cm Secteur, the stock parts were perfect. On my old dawes lightning, since I didn't buy it there, I had to pay $50 for the fitting. As part of that they swapped out the 1" quill stem for an adjustable hybrid style stem (its the only thing that was short enough and fit the bike while allowing the stem shifters to work). They didn't charge me for it and said it was part of the fitting.