We need to know a little bit more information.
Which distro are you using?
What is your kernel version? (in terminal, type uname -r)
What model of joystick do you have?
Although I can't really help you here since I have no experience with joysticks in Linux, that information will be useful to whoever can help.
Also, might I ask which game(s) you are trying? I would like to try using a joystick in Linux myself and would be happy to share my results. It is odd that a calibration utility would pick up analog movement and buttons just fine, but a game would not.
I am using MEPIS 6.5
I am not at home so can not check directly but the kernel is probably 2.6.15-27. Won't be back home for about another month so there is no real way to check for sure.
I have tried a Sidewinder Freedom, another one with a big ball joint in the middle so the two halves swivel independently, a cheap Genius with either 3 or 4 analog axis and maybe 8 buttons and a hat switch. I think I tried my Logitech Freedom 2.4 but don't recall right off. Probably a cheap Genius driving wheel with pedals also. The all do the same thing.
As for games, I have tried Search and Rescue, well, I am having a hard time remembering the names since I cant look at my menus. I think I have tried TORCS in the past. A couple other driving games and some flying 'sims' and arcade games that are supposed to support joysticks.
I could probably understand if the occasional game wouldn't work but I can't seem to get anything to work except for the calibration utility.
I am on vacation and will not be able to answer any specific questions till I get back home but will try to answer any questions the best I can.