Okay, the main thing about the Boss pedal (and I'm guessing other similar noise gates) is that you DON'T just plug it in like a normal pedal, either in front of the amp in the effects loop.
You chain should look like this:
guitar -> NS2 input -> NS2 send -> other pedals -> amp input -> amp effects send -> NS2 return -> NS2 output -> amp effects return
The idea is that the gate is controlled by your clean signal up front, but cuts off the signal at the very end of your chain after distortion has been applied. If you use it this way, you can basically have total silence when you're not playing even with potentially infinite gain, assuming your guitar isn't picking up hum directly.
Great post, and really should be the way to do it. I'm lazy and just put it in the loop, works fine to get the amp noise out...for the rest of it I just learn to play clean

~006