Can't talk much about gamepads, but if you're talking flight sims for DOS, there are a few ideal setups:
-Thrustmaster F-16 FLCS/F-22 Pro + F-16 TQS
-Thrustmaster FCS + WCS Mk. II
-Suncom F-15 Talon/Eagle + SFS Throttle
If you're wondering why I don't mention CH Products, it's because they use a button matrixing scheme on the Flightstick Pro and later (and Suncom's SFS Stick is functionally a CH Flightstick Pro sans throttle rotary) to support their hat switches that makes simultaneous discrete button presses impossible. Try firing missiles in Wing Commander/Privateer on one of those!
Just throw in whichever gameport pedal setup you'd like (TM RCS/Elite and CH Pro Pedals are easy enough to find, Simpeds are ideal but uncommon and expensive), and you're good to go.
If you can't go full HOTAS and pedals like a flight sim deserves, perhaps for space or cost reasons, pick up a Microsoft SideWinder 3D Pro.
It can emulate a TM FCS or CH Flightstick Pro + pedals in analog fallback mode (which means you're trading off your throttle slider or simultaneous button presses on a per-game basis), and it also uses a central optical camera + LEDs for all four axes, so you never have to worry about spiky potentiometers. They're also ridiculously common and cheap as chips, easily found in thrift stores.
Later SideWinder sticks like the Precision Pro are not an option because they axed analog mode completely, and thus will not function in DOS.