Well, in winter is the cheapest time to fly to Portugal because it's the time when Portugal has less people visiting the country. After there is the "low-coasts" trip, but in Portugal the best company is TAP.

Yes, the fall is the less expensive time to go to Europe. I have a suggestion as far as the accommodation is concerned. If you want to stay in a charming historic place in Portugal you can do it at one of the pousadas. These are government owned and operated former mansions and castles, restored and converted into the beautiful hotels. They are ideally located in the historic cities or rural areas of outstanding natural beauty. They offer high standards of comfort and service, delicious food. Check this link for more information: link. You can also book pousadas through the tour operators. Escapade Vacations: www.escapadevacations.com or ATOP: link. They offer special packages including air and the car rental.