I have bought several space simulators in the last few months (X-series at Steam, Freespace 2 and Wing commander here) but I'm still having some difficulties with ship control. The keyboard and gamepad sticks are good for "rough" movements (like turning around) but a mouse brings more precision (for example, targeting).

How is it to play with a joystick? Is it much better than a gamepad?

Yes, in my opinion a good joystick is usually better than a gamepad for this kind of games...
This is even more noticeable with the older ones (like Freespace and WC), while some recent ones do implements smooth mouse controls (for example the X series until X2 included plays better with a joystick, while X3R and X3TC controls are equally nice with a mouse)

On a side note: nothing beats a HOTAS flightstick in terms of pure immersion

That's why I'm hesitant not only I'll need buy a Joystick just to play few oldies but also most chance is I won't be able use it when playing on Mac with some wrapper, mostly DOSBox. Too bad Wing Commander 3 (3DO) was good memory.

nothing is better than a mouse.. look at my WC1 perfect score thread...

what??

I would go for a new joystick as well. I recently received my X65f and play simulations i a completely new experience. I can even play Privateer...which sucked with every imput method I had tried before.

DOSBox joystick support is pretty good now. You can even remapp buttons with STR + F1 without any additional software. Of course, a sepparate mapping software enabled further possibilities...