You can't file a joint return unless you both agree. It sounds like that is out.
If you separated in November, then neither of you can file a head of household, you must both file as married filing separately. When married filing separately, you can only claim the personal exemption for your spouse if her income was less than $4050 and she will not be filing a tax return. (Spouses are never dependents, but you can sometimes claim the spouse's personal exemption, which is similar.)
For your children, you both could claim the children as dependents since the children lived with both of you more than half the year. However, a child can only be claimed by one taxpayer. If you both claim the children, the first tiebreaker is with which parent did the children live more? (Stay the most number of nights in their home.) If your wife had more custody than you after the separation, then she would get the tiebreaker if you both claimed them as dependents. If you had custody more nights, then you can claim the children, and if custody was exactly equal number of nights, the second tiebreaker is the spouse with the higher income.
