You can use modern joysticks/ joypads on anything that runs on an emulator, like DosBox. (And GoG versions of WC games, run on a modified version of DosBox). You can also use them, in any Windows game, that supports DirectX (nearly every game after 1997, that is 🙂 ). So yes they will work!!.

 

 

when I'm playing Wing Commander with it. I want to go back as far as to the first game in the series. 

Although GoG version are fine, I prefer the "Kilrathi Saga"  ( http://www.mobygames.com/game/windows/wing-commander-the-kilrathi-saga )compilation, for the first three games of the series. (And you new joystick will work fine. I finished WC1 with a HOTAS setup).

 

 

Also as far as I know TIE Fighter doesn't allow you to play it with a keyboard...only with a joystick.

There are two versions of TIE Fighter. The Dos one (so you can play it with DosBox), and the Win95 one (You can still play it using Windows). So newer joysticks also work.

I vividly remember successfully using a Saitek X52 to play X-Wing vs. TIE Fighter and X-Wing Alliance, but I don't remember if I had to jump through any hoops to get them working.  There is some issue with the installer though: the installer for all the old Lucasarts games is 16-bit and for some reason is fundamentally incompatible with 64-bit operating systems, so they don't work.  Fortunately, the games themselves are 32-bit, so if you scour the internet somewhere you can find a guy who wrote 32-bit installers.  If you've already resolved this, it might be good to post a link to how you fixed it for posterity...