My controller came today.. made on 7/22/11 so its fresh and new. Will be cutting away the alarm function wires. I'd like to use the previously mentioned red and black wires for a voltmeter, but the voltmeters need to run off 5v DC power, which I have no clue where I'd get such power from. Once I get in my motor, I'll see if it runs in 60 or 120 phase then I'll know if I can just snip away the phase degree wires.
There's been a lot of clutter on this thread about which wire does what so I'll take jonathanm's picture and make a better diagram including all the uses of each wire.
Cruise Control: Wire a momentary switch to it, and lead it to ground. When pressed, cruise control is enabled.
Voltmeter: This is simply wires that tell you how much battery voltage you have, so you can lead these to a voltmeter if you want, or snip them away, but make sure its neat since it carries all x amount of voltage that you have in the pack. You can use the alarm wires instead if your voltmeter requires 5v DC. Another use of the voltmeter wires is a DC-DC converter so you can run your aux lights/fans.
Alarm: One wire has 5v, another has your battery + voltage, and the third is ground. Use it for a voltmeter if you'd like, such as this
Hall and Sense: Depending on your motor, you may need to use the guide previously posted to figure out which wires you'll need to switch around.
Throttle: Same thing with throttle, sometimes they'll need switching around but try it first to see if it works without modding.
60/120 wires: Auto its 60, if your motor runs weird, try 120 by connecting the two wires together. If you don't need them connected, simply snip them away.
Ignition: This can either be wired to a switch, that goes to your power supply +, or you can connect it directly to power supply + if you wish to have no switch for ignition.