Which is better for me to do, filing jointly with husband or separately?...?

My husband & I were getting a refund of $3000 total fed and state until I added his income and the 1800 stimulus from last year. Now it says we owe over $3000 when I added his, filing jointly. Do I have options? I can't afford this.Should I we file married but separate as we have been separated since Dec. 19, 2007 and still are? Or should we file separately?