While most married couples file jointly, there are instances when filing separately will result in a lower tax bill. For example, if one spouse has high medical bills or has debts from before the marriage that are past due, such as child support, these debts could be collected out of any tax refund. If you file separately, the debts would be collected out of the responsible party's refund, rather than out of a joint refund.
One thing to remember about filing separately: The IRS requires that both spouses either itemize or take the standard deduction -- if you itemize, your spouse must itemize, too. You can't itemize on one return and take the standard deduction on the other.