Some controllers have a fourth pin which is the battery's full voltage. make sure you identify that one.
A multimeter could come in handy.
in your case you are describing only three wires, so i would theorise that you only have a ground, +5v and the wiper which is 0 to 5v, just as CowTownPeddler mentioned.
The way it works: the throttle receives a stead +5volts from the controller through one wire, that potential diference is realise by having a ground from the throttle to the controller. When you twist the throttle, a wiper moves across the resistor's length and modifies the resistance on the circuit and therefore returns a percentage of the +5volts back to the controller. The controller then interprets that range: 0volts as no power to the motor and +5 volts as maximum power. If you have a cycle analyst you can actually fine tune this range as not all controllers will give out exactly 5volts (you may read 4.5 volts as maximum .. but ususally it's around that valu of ~ 5 volts. )
Here's how I know about this. While upgrading from a 48 to 72 volt setup, I blew my controller and the throttle and everything along that circuit. So, I got a new controller, but my throttle was dead, so had to improvise. So I went to the electronics shop and got me a variable resistor, comes in the form of a dial which has three pins.
In my case , I had a fourth wire on my new controller, lucky me. One of those pins is the full voltage of the battery. MAKE SURE YOU IDENTIFY THAT ONE.
* I made sure to stear clear of the one that had the full voltage across the battery.
The voltages on those three other pins is quite small (provided you stear clear the above *). So I connected the throttle pins to those of the controller , and tried every combination amongst those three pins until it worked, (again making sure to stay away from the fourth pin on the controller). And it worked! In my case the controller's wires were not coded the same way as the throttle's.
My controller is a digital one from crystalyte, high power 72 volts, 35amps.
The colours on that one are : RED, ORANGE, YELLOW, WHITE. *White is the full battery voltage. I stayed away from that one.
So in my case, i connected my throttle this way:
THROTTLE --> CONTROLLER
------------- ----------------
RED --> RED
YELLOW --> ORANGE
GREEN (wiper/throttle) --> YELLOW
Hope that helps.