I have gone through the default windows calibration menu like a gazillion times and everything works fine, except my c stick. It is always recognized as slightly to the left and any small movement is recognized as pushing the stick further than possible
Calibrating Gamecube C-stick
controllersemulationnintendo-gamecube
Related Solutions
The original version of GTA3 used a button, and not a analog stick axis, for both throttle and brake. On the other hand, the DualShock 2 had pressure sensitive button support, so on the PS2 they were more like analog controls than digital buttons.
However, most of the ports of GTA3 don't support analog throttle/brake for whatever reason. It might be possible to use a controller remapping program (AutoHotKey is my go-to for this, but I think Controllermate might fill a similar niche in OSX) in order to change this behavior. However, it's likely to break other things you'd want to do with the right analog stick - like looking around when you're on foot, for example.
I think in the end you might just have to chalk this up to a missing feature in the ports of GTA games.
Solution: Uncheck "Xbox Configuration Support" in the Controller Config menu in Steam.
Recently Steam announced Controller Config support, similar to the Steam Controller profiles, for Xbox controllers. When this announcement happened, I started playing around with the settings. I set this:
I forgot about it. But that was the problem. I just disabled it and everything is fine again.
Best Answer
On a real GameCube, you could cause the various analog inputs to recalibrate by holding down X, Y and Start for 3 seconds. If the problem you're having is only within Dolphin, this should clear it up.