Hi there,
is there any way to invert the Y axis of the mouse in Freespace 2?
The only mouse related option I saw in the menu was to turn it on, or off.

Launch FS2. Go to "Options", "Control Config". Select "Ship". Go to where it says "Pitch Axis", at the very bottom. It should say something like "Joystick/Mouse Y Axis". Highlight that and look to the bottom left where it says "Alt" "Shift" and "Invert". Select "Invert" and enjoy.