the inspiration for the term may have originated as a mockery of an idiot school board, but it's subsequent applications, at least as far as I've seen it used, are most often as a counter to monotheism, and almost exclusively toward the 'Christian' God. I'm not a very religious person, and not even close to being a 'holy roller', and by my own personal experiences and conversations, I've found that the great noodled one to be consistently used as a barb toward Christians. many people who believe in God find their deity's comparison to Italian pasta to be offensive, regardless of the origin of the term.
laughter works pretty well, too.