IMO.... all other things being the same:
a #'s matching factory 4 speed is worth more than a #'s matching factory auto.
a #'s matching factory auto is worth more than a non #'s matching factory 4 speed.
a non #'s matching factory 4 speed is worth more than a non #'s matching factory auto.
If you're looking for a car that will be worth big dollars when you get done, you'll want a numbers car with all matching documents (cowl stamping, radiator stamping, door VIN, Dash VIN, Fender Tag, Build Sheet (if it's a hamtramk car) and clean title). Look for 4 speeds or any 440 or Hemi car. Depending on the condition be ready to spend between 30K to 60K on top of the purchase price to restore the car back to factory specs. Stock restorations on big dollar cars will bring the highest resell.