I've worked either full or part time in bicycle shops for around 12 years now, and have been actually following bicycle blogs for a few years less than that. In that time I've heard a lot of complaints about poor service and the difficulty in getting shop employees to understand just what the customer is looking for.
Unfortunately, some of this is just due to a lot of shop employees being inexperienced at retail, or racers who have a hard time imagining folks doing a different kind of riding than what they're into. There's not a lot that can be done about that, but it might be helpful to understand a few things about the rest of what goes on in shops.
Price - One of the biggest problems a lot of us face is simply affording a new bike, this applies to shop rats as much as any of our customers (maybe more so, bike shop salaries are nothing to brag about). Unfortunately the bicycles are sold on a fairly thin profit margin. As fuel prices have risen, the cost of shipping has increased as well, further cutting into profits. Local bike shops can't raise their prices too much to compensate, because they're already being undersold in many areas by large online retailers, so that means entry level bikes are often sold at just above cost.
Because of this, there is very little room to haggle over price, which makes it frustrating for shop owners when customers come in with the idea that there's more wiggle room than there really is. Some businesses are based on the idea that price is negotiable, but the bicycle industry isn't.
This is not to say that customers shouldn't try to get the best possible deal, though! While the margins on bicycles range from "sad" to "nearly imaginary" the markup on parts and accessories is often much better. Because of this, if one is buying a number of accessories or upgrades shops can often offer a "package deal" on all the extras. If you're a good customer who's brings repeat business and a good attitude, a good shop will bend over backwards to give you a fair price and go the extra mile on service. Like a lot of small businesses, bike shops live and die by their repeat customers, and will try to take good care of them to keep them coming back.
On the other hand, like many embattled small businesspeople, bike shop owners can be stubborn, and trying to get pushy won't usually get you very far. And those razor-thin margins mean you might not have a lot of leverage. After all, when a customer says something like "I'd hate to see you lose a sale because you can't knock $50 off the price" the owner might come back with "I'm only making $45 profit on this bike, I won't lose any sleep over not selling it at a loss" (the language might be different, maybe).
On a final note, there's this whole internet thing. Sometimes a bike shop just can't beat the price of a Performance or Nashbar type shop. Heck, sometimes these big online retailers sell stuff for less than we get it wholesale! Every shop employee knows you buy stuff online, sometimes, if it's something our distributors don't carry, we buy stuff online too. Don't lie about it. In fact, we'll be happy to assemble that bike you bought online, for a reasonable fee, or do other work on things that come from an internet retailer, just as we'd work on a bike from another shop. The one really, really tacky thing to do, though, is to use the time, energy and know-how of your local bike shop to help you make an online purchase.
What I'm talking about here is coming in with a million questions about components, fit, materials and riding styles, getting measurements, test riding bikes and spending anywhere between a half-hour and two hours tapping the expertise of your local shop, then taking what you learned and buying your bike somewhere else.
A Little Knowledge - There's an old saying that states that "a little knowledge is a dangerous thing." What this means, in the context of a bicycle shop, is that just because someone read a couple articles or asked a few questions on internet forums, sometimes they think they're armed with all they need to know to get the perfect bike, and they can somehow outsmart the shop employees.
First of all, the shop employees, in a good shop anyway, aren't in competition with you. They're not trying to trick you or force something on you that doesn't suit you, they're trying to make sure you get a bike you'll enjoy so that you tell your friends how great the shop was and recommend them, and you'll come back happy and buy more stuff. Yes, they may have very strong opinions (may? will), but that doesn't mean they're trying to fool you.
A good bike sale is collaborative. You might have some ideas about what you want, the shop employee will listen to that, ask some questions and make a suggestion or two, and finally, give you a couple of options that you can check out and hopefully take for at least a short test ride. Eventually, the two of you will figure out what suits you best, although the shop guy might say "you'll really love Bike A" and you say, "hmmm, I kinda prefer Bike B." That's OK, it's your bike, and you're riding it, not the shop guy, but don't dismiss his opinion. Also, pay attention to the shop's "go to" bike for your particular riding style. Often there's one model that the shop has found offers the best value and suits the broadest range of riders. They'll often stock up on these and recommend them to a lot of riders, not because that's "what they have and they're trying to push them" but because "we like these and think most people will enjoy riding them."
These are just a couple of starting thoughts, but I welcome questions on other aspects of the shop experience, what do you worry about? What annoys you? What do you really want to know?