Whay to do if my seperated wife wrecked into her brother in laws car and did $3k in damage?

Since you are the registered owner of the vehicle, you are liable for your wife's accident.  As the registered owner of the vehicle, you would be obligated to pay the deductible.  You could sue your wife from whom you are separated, for negligence to recover the deductible and for the cost of repairs to your car.

In addition to the deductible and the cost of repairs to your car, your damages (monetary compensation you are seeking in your lawsuit for negligence) would also include the cost of a rental car while your car is being repaired.  You will need to mitigate (minimize) damages by having your car repaired at an auto body shop whose charges are comparable to other auto body shops in the area.  If you were to select the most expensive auto body shop you could find, your damages would be reduced accordingly.  The same also applies to the rental car.  In order to mitigate (minimize) damages, you will need to select a rental car with a reasonable rate.  If you were to select the most expensive rental car you could find, you have failed to mitigate damages and your damages will be reduced accordingly.  Depending on the amount of compensation you are seeking in your lawsuit for negligence, you may be able to file your lawsuit in Small Claims Court.  Your damages would also include the court filing fee and process server fee.