Choosing a bike shop

Not all bike shops are friendly and knowledgeable, as you've probably experienced. There is no uniform code of conduct for shops, no certification body for mechanics (aside from UBI and a few other for-profit bike schools, but all they really give you is a piece of paper for the wall) and there are no rules for what building and preparing a new bike entails. But when you walk into a shop, there are some guidelines that should let you know right away if the shop is any good.

1. Are the tools cleanish and organized? This is very important. If a mechanic doesn't respect their own tools, they won't respect your bike.
2. Are the tires of the for-sale bikes pumped up? Tires do lose air pressure over time, but not all of it. A good shop will check their inventory to know that everything will work fine if a customer wants to go on a test ride. If the tires are completely flat, then is doubtful the bike has ever been test ridden and there's probably something wrong with it.
3. Do the salesmen and mechanics audibly talk trash about your bike or cycling skills? When I was a BMXer I went to Rasmussen Bike Shop in Des Moines and the owner told me the reason I was bending rims was because I didn't know how ride right. 12 years later and I still don't shop there.
4. Are you helped promptly and not pressured into buying stuff? This is just basic customer service that all retailers should have.
5. Will they fix any bike, regardless of their own preferences, and let you know if the repairs exceed the value of the bike? Shops that don't do this are either snobs or rats and should be trashed on Yelp.

Bike Library of Iowa City

In addition to this there are other things to consider when choosing a bike shop. Brands matter in that certain brands are attracted to certain shops, and thus a certain customer.

Trek, Specialized, Raleigh, and Giant tend to like big shops that move a lot of volume. If you only have one shop in town, it will probably be a Trek, Specialized, or Giant dealer because they make a lot of marketing, sales, and training resources available to their dealers. Some shops will take advantage of the big brands' support and trainings to better serve their clients, others will use it as a means to fatten their pockets.
Surly, Civia, Foundry, and All-City are sold through the distributer QBP and do not have "no-compete" contracts with shops, so unlike the big brands everyone can sell them. They're most common in smaller and newer shops.
Serotta, Litespeed, Eriksen, Guru and custom builders generally live in fancy shops. Expect a coffee bar on the premises but there's no guaranty of better service. Sometimes a mechanic will get it in him/her that because s/he works on $10,000 bikes they're better than the mechanic in the Ma & Pa. I can assure you, this is rarely the case: expensive bikes are easier to work on.
These are generalizations, of course.

The very best way to choose a good shop is to talk to people. Bicycle retail is a grass roots industry and if a lot of people approve or disapprove of a shop there's probably a good reason for it. Look for a shop that's involved in the community, sponsors rides or races, and tries to get people involved in the sport of cycling and you'll probably find a good shop.