The first thing I think of is your ductwork or something else expanding when your funace comes on (or pipes if you have hot water heat system). Try to determine if your furnace is running when this happens. If you have hot water baseboard heat, this can happen from the pipes heating up and expanding and then they chafe and/or rub etc. at places where they come into contact with either mounting clamps or even the plywood subfloor. If your pipes are touching the plywood subfloor it is quite common to get these popping noises. If you can access these spots then try to get some black foam pipe insulation, or even some spray foam insulation in there with a straw. Don't go to all this trouble if you can't definately correlate the sounds with the pipes heating up with a furnace cycle. These sounds could be any number of other things. You have to try to be as deductive as possible to try to relate the occurance with some other factors (or eliminate factors). I.e.: does it only happen when it gets below 40 deg (possible thermal shrinking of frame). IF it has been warm that day? Does it have to be windy out (house swaying b/c of inadequate wind bracing)? Are you 100% certain it DOESN'T happen during the day - or don't you notice it b/c there are 1000 other noises or because you aren't IN the house during the day? You need to be sherlock Holmes and get some more reasoning going. Also, give us more to go on, all we can do is guess.