My wife and I were legally separated for all of 2006. We know we can file a joint federal return but she needs to also file in Georgia. I lived and worked in Texas the entire year. Can we file a joint federal return and file it with the IRS, have her fill out a federal return as a single person and send that in with her Georgia state return? I have had nothing to do with Georgia and just don't want to be involved with them or have my name associated with their tax system.

File jointly in Georgia as a part-year resident. That way, you will file legally (your optiont to have her attach a SINGLE person return to the GA form is TAX FRAUD), but you will only pay taxs on HER GA-based salary.