I am an accountant (a CPA), but as a disclaimer, I do not do taxes as a part of my job and am not a tax expert. The only thing I know is what I need to do my own taxes and what little I remember from memorizing for the exam and from school. That said, there are some specific circumstances when it is advantageous to file seperately. I could not answer your question though, without a lot of specific information that you probably would not want to share over the internet.
I am assuming that your income situation is fairly simple (i.e. w-2 income, retirement savings, home mortgage interest). If that is the case, go buy Turbo Tax or something equivalent. Most people's taxes are fairly simple and can be done in a few minutes, but Turbo Tax will catch little things that most people will never think about. It will also prepare the most advantagous filing based on the informaiton you give it. It is definitely worth it, and will save you time each year as it keeps the details from previous filings to help you. And no, I don't work for Turbo Tax.
If you have multiple or complex sources of income, or you are jointly making more than $150K, it may be worth it to see a tax professional. Not only can they help you prepare your taxes to maximize your refund (or minimize your payment), but they may be able to give you additional advice that can save you money.
NOTE: whatever method you select to file for Federal (joint or seperate) you will need to follow for your state. So in order to determine which is best, you need to do both returns each way and compare them together.