We live in an old farm home in the country and have a very serious fly problem. We keep our house very clean and our garbage is kept in a closed container until it goes to the dump each week. I've tried sprays and fly paper which both work temporarily. Within days we have hundreds of flies in our house, gathering mainly around windows, and they seem to be worse upstairs.

To end a fly problem, you must eliminate the breeding source, an organic source, perhaps a dead rodent. If this is an ongoing seasonal problem, the source is not inside your home, but outside. Spraying the exterior walls monthly with Demon Wp,   or  Cyonara 9.7 will help control them.
If this is a new problem, you may have a dead rodent in the attic or in a wall. If you can't remove the rodent, time will take care of the problem as it decays.

I am having a lot of fruit flies due to my having 10 birds with a lot of food and fruit available at all times. Any suggestions as to what I can do?

  Clear Zone Metered Aerosol is a pyrethrin based aerosol that is safe to use around birds. It will help to control adult flies, but removing the food source is the only long-term answer.