Measure out about a foot and half worth of wire from the neon tube. Take a scissor and cut it (or chew it off if you're the barbarian type):
Take the two small wires that come out of the molex and strip it about a centimeter. Do the same for the wires from the neon tube.
The neon tube wires are not colored, so you won't be able to tell which line is the 12V and which is the ground. What I did notice is that the 12V line had a white line down the side and the ground didn't. The line may be there to tell you that its 12V, of course I can be totally wrong which is quite frequent. Anyway, connect the 12V line to the red line (color may be different for you) of the molex connector. If you are un-sure of what that means, check out my Molex Connecting Guide for a cram course on wiring.
Tape the bare wires together or use heat shrink to prevent any oddities inside your case. Plug it in and BAM (Emmeril?), you got a nice light show inside your box!
Now wait, I don't want to leave this damn neon light on all day and all night. I can barely see the damn thing during the day anyway! Time for a switch courtesy of Radio Shack. Use this diagram to guide you to the right way of wiring a switch to the tube, a lot like wiring a fan actually:
You can probably do this with a SPST (?) switch, but I had a SPDT switch left over from my FanBus Switch Guide so I thought I'd just use this one. Again, you can customize this to your liking, this is just a general outline. Skip this whole step and connect this to a fan....errrr Neon Bus! Now that will be a site to see.