Can you file a joint tax return after you have been legally separated?

If you both agree to file jointly then yes of course.

If you are married at the end of the tax year for which you are filing the return - even if you are not living together - you can generally file a joint return. You both have to sign the joint return and the rules regarding liability for signing the joint return will comply. If the legal separation ultimately results in a divorce you will of course lose the option of filing a joint return.

There may be future reasons for not filing jointly, especially depending upon how close you remain and how much actual knowlege of each other's operations you both are comfortable with. (i.e. if he starts a business or invests in a tax shelter, it might make a mess for you).

No, you cannot do this, certainly not for federal income tax purposes and most likely not for state income tax purposes either (I don't practice in Arizona so I cannot properly answer under Arizona tax law). For the purpose of filing a joint federal income tax return, under section 6013(d)(2) of the Internal Revenue Code (the section that governs joint returns) "an individual who is legally separated from his spouse under a decree of divorce or of separate maintenance shall not be considered as married...." Thus, if you and your estranged spouse are legally separated under a decree of separate maintenance as of the end of this year, or any future tax year, then you will not be treated as being "married" under sec. 6013(d)(2) and will therefore not be allowed to file a joint income tax return with your estranged spouse. As this is a matter of federal law, which controls over any state law to the contrary, you cannot change this result by having a provision in your separation agreement that mandates continued joint filing.