I worked in a bike shop about 15 years ago, and at the time our cost for bikes was about 60-65% of the retail price, but like other posters have mentioned there is some additional labor involved in putting the bike together (not to mention the overhead of the store).

When I was shopping for a bike, I called every bike shop (there are a lot in my area), or looked on their web page to find the best price on the bike I was looking for. I then took this price to my LBS and asked if he could match it. They couldn't quite, but came very close and offered me free service for life, so I went with the LBS. I think in most cases you should be able to negotiate around 10% off, or some kind of upgrade such as better wheels.