I recently had all of the cables replaced on my cyclocross bike. When I got it back from the shop, I installed a new wheelset. The first time I rode it after that, it was making terrible creaking noises. I rode for about 2 hours and the noises were so annoying that it was driving my crazy. I assumed the noises were the new wheelset, but the noises continued after I swapped out another wheelset that I knew didn't make any noises. So I brought it back to the shop that had replaced the cables. The mechanic took my bike for a short ride and quickly diagnosed the problem -- the seatpost rail clamp. He figured that out by standing up while riding and noticing that it didn't creak when he did that.

It all made sense then, because I had forgotten that I had recently swapped saddles on that bike. The noises immediately disappeared after I properly tightened the seatpost rail clamp.