I've owned a 2000 S80 and had no problems with the car-except for the front subframe bushings that was repaired under warranty- and bought a 2005 S80. There were big changes on the '04 S80 even it doesn't appear so. The resale on S80's isn't very good which should make buying one used a good value for you. I would look for a used '04 over a '03 b/c of all the changes although I wouldn't pass up a good '03 if one came along. The '99 to '00 models seem to have a fair share of problems but later ones seem fine. A good dealer to service your car is the key here. A dealer can make your experience either enjoyable or horrible when it comes time for service.
Bottom line-an S80 is a safe and comfortable car with no more problems than a typical european car and that includes BMW, Merc and Audi.