Is it best to file jointly or separately during a divorce?

I'm in the middle of a divorce. We separated right before the holidays and the divorce was filed after the first of the year, so I was still married for all of 2008. My soon-to-be ex-husband is a self-employed independent contractor who should be filing quarterly, but doesn't and usually ends up with a penalty fee. I'm a grad student who works part time for the university. I usually get a refund and we apply that to my husband's taxes, which are usually quite a bit. Beyond that, I have to review the old tax records. I haven't filed my own taxes in over five years, so I would greatly appreciate everyone's advice on this matter.