I remember playing Freespace 1 a long time ago with a joystick and it worked just fine, main problem for me then was that the Freespace CDs I had were buggy and one of the missions just wouldn't finish and if I tried to jump out it said that I had failed. The day (years later) that I found out there was a patch released is one of my fondest memories as a gamer :)

Anyway I'm getting sidetracked, do you think it can be an issue with modern joysticks in general? I'm thinking about getting one but if Freespace is not going to work properly I might rethink the whole thing.

Well for Freespace 1 I would agree with the recommendation to use the FSPort in Freespace 2 Open. Improved graphics and bug fixes. You can even use TrackIR. I use PPJoy to combine my stick, throttle and rudder pedals

With the new installer it is a lot simpler to get it all up and working

http://www.youtube.com/watch?v=iVBj1QVHbNw

http://www.hard-light.net/forums/index.php?topic=87537.0

List of upgraded campaigns

http://www.hard-light.net/forums/index.php?topic=58358.0