David, I was looking for that answer once. I found a comment that said, "if the bottle is going back into the fridge, don't make the stopper too tall." I got to thinking about that, and now when making them, I carefully measure the depth of the threads, and make it at least 1/4" longer if I'm going to make a short one. Most of the time the ones I make are at least 1 3/4 - 2 1/2" long.
But, it's a preference thing. You make them to suit what you think looks good. ............ Jerry (in Tucson)