I have a dilemma getting my controller setup to work. After messing around a bit, I think the best way to handle it might just be to use use software to map my controller commands to the keyboard. Unfortunately, I can't find a command for rolling with the keyboard. Needless to say, while the game might be playable without rolling, I really don't want to lose that part of the experience.

Is there a key to make this happen some how?

I can't find anything in the documentation, but you can try holding Shift or Ctrl or Alt and then pressing left or right.

There are keyboard commands for roll but for some reason they get disabled if you use any kind of joystick.
The only alternative is to disable joystick support in the game options and map everything using keyboard commands but you'll lose any analog function for the movement axes.
Basically it's either keyboard only or "hold button 2 to roll" and nothing else.

Doesn't seem to do anything. I found an old manual with completely different controls for basically everything where Ins and Del are supposed to do it, but they don't work either. I don't think there is any analog joystick support anyway, so I'm fine with just mapping it to arrow keys. What keys have you found that will work for rolling?

There is (I played the game with a joystick from start to finish), you need to turn the joystick on in the options in the main menu if it isn't already (it should be by default), just go in the options and disable the joystick and INS and DEL should work for roll.
But sincerely I don't think it's worth it, basically all games at the time that weren't hardcore flight simulators only supported two analog axes and so you had to hold a button to roll using the mouse or joystick (usually button 2 on mouse/joystick), it's a limit of the way joystick were programmed at the time.

The roll commands on my keyboard are 'Home' for counter-clockwise and 'PageUp' for clockwise roll of the ship.