I am having some trouble with this game as far as using my Wired 360 Gamepad is concerned.

I have selected the gamepad in the configuration options, but once loaded, the game will only respond to my keyboard and mouse. I must be doing something wrong, as no one else seems to be having this problem. >.< Please help!

This is what worked for me Open Regedit to the following:

HKEY_LOCAL_MACHINE\SOFTWARE\lucasarts entertainment company llc\star wars starfighter\1.0\InputDevices (32 bit)
or
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\lucasarts entertainment company llc\star wars starfighter\1.0\InputDevices (64 bit)

Then change NumJoysticks from 0 to 1, it should recognise the controller ingame now.

Worked for me, but the config seems to shift in game. Buttons act how they should in the menus, but once in game the buttons seem to shift, for example A becomes Y...anyone else having this problem?

Yes, exactly this happened to me too. I can't use my Wired 360 gamepad on Starfighter, then I changed the registry value as you suggested and now I CAN use it but the buttons are all really weird!

I'm apparently getting this same problem. For me, I have vJoy installed so there is always a controller enabled. The game detects it though without the input into vJoy enabled it has no input. The keyboard buttons don't seem to do what they are supposed to, though. E and R are supposed to be roll left and right, but E accelerates without boost and I cannot roll. Very strange behaviour. I'll try disabling my vJoy in the control panel to see if that makes a difference.

UPDATE: Disabling vJoy in my Device Manager resulted in the game not even detecting my keyboard! :(

Yeah, I'm having the same problem i'm not using a 360 controller so the ingame defaults aren't too bad but any changes i do make don't stick past the menus. I'm still trying to figure out why though.

I am also interested, how I can play with my Xbox360 controller. Tastatur and mouse aren't the best solution for flight games. But the game is new on GOG, maybe later an update comes out to fix this problem. I hope so.

It looks like it is a registry entry problem. A combination of missing entries and the game reading from one set of keys but writing the settings to another, apparently. See the below two threads:

http://www.gog.com/forum/star_wars_starfighter/major_control_problems_with_this_game/page1

http://www.gog.com/forum/star_wars_starfighter/how_to_fix_your_controller_problems

Yep, this works nearly perfectly. You may need to go into 'Configuration Options' afterwards to assign a couple of buttons ('Auto Target' in particular is vital) but otherwise it works fine.

Since this game was made way before the Xbox 360 Controller (and XInput) came along, may it be that it only natively supports DiInput gamepads?

Obviously glad to see that there are workarounds for the 360 controller though!

XInput controllers operate in a DirectInput mode for older games that don't support XInput.
http://pcgamingwiki.com/wiki/Controller

I, myself, have used a 360 controller in a number of older games. What I've found is that it works, but you get some oddities. Like the lack of deadzone and sensitivity settings so the thumbsticks are sometimes not great, and the right thumbstick mappings are off, so that on the right thumbstick the vertical movement operates what should be a horizontal movement and the horizontal movement itself does nothing (evident when playing flight sims and space sims where the right thumbstick is to roll the craft yet you move it vertically to do so, against what you would expect). Additionally, the two triggers are a single axis in DirectInput mode, so with both released the axis is at 50%, same as them both pressed fully down. This can be a little jarring when they are set up as a throttle/brake.

Recently I moved to using vJoy to take the XInput controls and to remap them to a virtual controller using Universal Joystick Remapper. This gives me a new XInput (virtual) controller where I can set the deadzone and sensitivity and swap the right thumbstick axes so that all of these then operate fine in game. I'm sure the triggers can be split, too, but I've not tried that yet.

So I wouldn't say the issue is due to the game only supporting DirectInput as 360 controllers will operate in a DirectInput mode (although without tweaking I find it quite lacking). There is a known issue with the registry entries, though, which I'm disappointed to say that even though I have sent the full details to GOG Support, there has been no updated version of the installer released.