I pay more attention now to how close the spouses are to the line where Medicare premiums increase by at least 50%.  If one spouse has income of $120,000, the other $90,000, a joint return is going to raise premiums for both of them.  Separate returns might not save any tax, but is it worth saving $1,000 or so in deductions from the Social Security check?  

Others covered the common situations.  The 7.5% limit on medical might work for one but not the other.  The 2% on miscellaneous, before it went away for a while so corporations could pay less tax.  The unemployment exclusion, where the income amount was the same for separate or joint.  The California millionaire tax, and whatever they do in Rust Belt Ohio.

Mentioned in another thread was the idiotic rule on cancellation of student debt when a public-service employee works like an indentured servant for a certain number of years.  Many must choose between claiming a child tax credit, or eventual loan cancellation. 

But MFJ should not be a knee-jerk reaction, especially when it's apparent that the couple will owe taxes and won't have the money to pay it.  A lot of innocent-spouse cases could have been avoided, by smart preparers.