Freespace 1 and 2 both work with joysticks and your modern operating systems - be aware some people have had compatibility issues with both (just like any old game), but in general they work. If you do have problems, come back, and post them here and/or contact GOG support to work through them.
They actually used to have an automated installer for the FSO engine, but unfortunately it no longer works. A new one is being worked on. However, the instructions for manual installation are not too bad if you want to give it a shot though I understand if you don't (
manual installation instructions).
I really enjoyed FS2 and FS1 - I played them through the FSO engine on my Mac, (the engine may be different, but the campaign content is the same). I also enjoyed some of the mods (especially the Blue Planet series), but they require the FSO engine. You can also download some the total conversion mods (for Battlestar Galactica, Babylon 5, etc ...) which don't require installation of the FSO over your copy of FS2 (it's all self-contained in the download).