One more vote for the QR skewer. Two of my friends have had creaky skewers. One front, one rear.

My bike developed a click. I believe it’s actually the pedals (the bearings don’t roll anymore, but I have yet to replace them so I can’t be sure that’s the culprit. But I’m fairly confident.)

check your cassette lockring as well. Also, I’ve seen hub axle end caps come loose.