for which game??? if its FPS then of course I'll choose mouse.. if it's FIFA then joystick it is.. be more specific?
Acually it depends upon the related game i.e. which one you are going to play now only.If you prefer play racing games like mostwanted or bike racing then you just go for the joystick or if you want to play IGI or mission like game then you just go for mouse.
If you're playing a game like Super Street Fighter IV, Anything Vs. Capcom, or any fighting game then a joystick/fightstick is the right choice. Also, any flying simulation games like Ace Combat or any simulator. But, use a mouse for everything else. It is faster, and provides better controls for aiming.
I use mouse(+keyboard) to play FPS game like Crysis 2, and I use joystick to play Pro Evolution Soccer 2011.. it's really depends on the game you play..
It largely depends on what game you are playing. You may want to use a mouse for some games and a joystick for others. I feel you have more control with a joystick. But for someone who has steady hands, a mouse may be a better option. It all depends on what you are comfortable with.