What is the proper form of address for a retired general and his doctorate wife?

Traditionally a general never really retires. They may retire from active duty, but they can be called back to service anytime by the President. Historically, military officers always kept their rank as a title but the idea fell out of favor after WWII, but it is still common and proper practice to address flag officers as general or admiral depending on their service branch.

A Ph.D., or an equivalent, is considered a professional designation and generally the people that hold them only use the letters or are styled as doctor in their professional lives. Also a person who holds a doctorate is never styled as doctor in written form, only verbally. When writing their name the proper way would be to use the initials after their name. Though it is also incorrect, to write Dr. Smith implies they are a medical doctor.

If writing specifically to the wife you would write:

Mrs. Jane Smith, Ph.D.

When writing both there is a formal and informal. For a formal letter, such as an invitation, the proper way would be:

General and Mrs. John Smith

Informally:

General and Mrs. Smith

Hopes this helps.