I had an issue when I got out of the saddle to pedal. Every pedal stroke there was that noise. I knew it wasn't the saddle or seat post and figured it was in the front end; adjusted my headset, handle bars, brifters, stem and tightened my quick release. The noise was still there.
Finally figured it out. My front wheel had straight pull spokes and no flange on the hub. Pulled the dust covers and put a drop of Phil's Tenacious Oil on each side. That stopped the noise from the spokes rubbing on the hub.
Any place metal meets metal can cause a creaking sound and in this rainy weather you'll wash away needed grease or in some cases pull some microscopic piece of grit in between the parts.
Nothing more frustrating than trying to find that noise.