I have been having strange issues with an ibike that I have built, in that interference keeps being generated from the motors phase wires into the RX/TX lines on the hall sensors. I have been advised to use shielded cable on the hall sensor wires back to the motor. Do I ground the cables' shield to the chassis of the bike which is metal, or to the ground wire on the controller/motor? At present, the motor/controller uses its own common ground and isn't grounded at all on the chassis.
Yes, motors generate a ton of electrical noise.
In grounding the shield cable, the main thing you want is for any charge that's built up to have some place to go very easily. This means you want low impedance and a big capacity to sink charge. Generally we get this with a big fat wire connected to ground which, in many cases, literally means terra firma. In your home you likely have somewhere an 8' metal rod shoved into the dirt and a 12-14awg wire connecting it to your electrical system.
For your application, you have a floating system. Your bike is more or less insulated from the surrounding environment. The frame is a decent sized capacitor, meaning it can sink some charge without much change in voltage. From your description we don't know anything about the motor but there's a decent chance it's ground is connected to the frame anyway. This would be easy to check with a multimeter. Either way will probably work.
If the shielding is insufficient, I suggest moving the power and signal wires away from each other as far as possible. This is standard practice. If you get really desperate, you might add a choke (http://en.wikipedia.org/wiki/Choke_(electronics)) to the motor drive lines to clean out some of the higher frequency signal.