Get several bids and don't always accept the bidder with the lowest price! As the saying goes - sometimes you get what you pay for.
Make certain that you are comparing apples to apples. Have them provide you with a detailed list of what is and is not included.
Pre-arrange financial agreements in writing.
Changes and extras are billed at what rates? Are they hourly or "piecework?"
Do they have proper Worker's Compensation Coverage? Are they paid up-to-date?
Ask for references.
Talk to previous customers and subtrades they have worked with. If they are a quality company, they will be happy to provide you with that information.
After these decisions have been made and it's time to get down to the actual building of your home, take the time to arrange a schedule.
Schedule material delivery and other subtrades. You have less time than you think and there's nothing worse than waiting for supplies because it holds up the entire building process.
Don't wait until the last minute to decide on your big items such as kitchen appliances or bathroom fixtures. Even though they are some of the very last things to actually go in - sizing for these items during the building process is important!
Buy local if at all possible.
If there are any problems they are right there to fix it or if you need more of a particular item they can provide it for you more quickly.