I recently bought Wing Commander 1 and 2 bundle. Is there some trick to getting the game to recognize my joystick? It's a Saitek x52 Pro. Is it because it's an entire HOTAS system instead of just a joystick?

It recognizes my Thrustmaster HOTAS just fine. Note that by default, it will only recognize the stick and buttons 1 and 2, since that's all a "joystick" was back then. You can use a program like Joy2Key to bind keyboard commands to the other buttons.

If it's not even recognizing the stick, though, then I'm not sure.

Logitech Extreme 3D here. Windows 7 sees joystick fine, all is calibrated and recognized in the settings, but Wing Commander won't use it.

Interestingly, DOSBOX reports that it detects and loads the joystick and all its axis and buttons.

EDIT - Figured out that DOSBox was mapping the joystick functions to my gamepad (I have an old Nostromo installed in this case). Went into the DOSBox mapper (ctrl-F1) after launching GOG's Wing Commander 1 and Selected the Joystick functions for the X and Y axis (both + and -) and buttons 1 and 2. I replaced each of the mis-mapped items to my actual joystick. Works like a charm now, just make sure you SAVE the mapping.