Having just gone through the process of buying a new acoustic guitar (I picked up a L'Arrivée D-09 Rosewood Standard), it struck me that this might be the best time to let others know what I consider to be the best method to undertake when buying a new instrument.
A few things to keep in mind before we begin:

Have patience - do not decide you HAVE to buy the guitar that day. Plan on taking at least two trips to the music store.
Maintain control - You are in charge! Don't let music store salesmen intimidate you.
Research - The web is a great place to find info on guitars. Use it to your advantage!
Get help - if at all possible, recruit a friend who plays guitar to help you choose an instrument. If not, don't be afraid to ask music store employees multiple questions.

You do not have to be an expert guitarist to get a good deal on a good guitar. What you do have to be is a disciplined shopper.