Originally Posted by TCR
It's the forward/back / pushing/pulling while seated on the saddle that causes the creaking noise. Pedaling, moving forward, sliding back, hitting a bump, shifting weight, etc all will cause the little creaking click sound.
I'm having the exact same problem on my Trek 4300. I haven't done as much homework on the noise as you have but if I grab the stem in one hand and the rear of my saddle in the other and flex up and down I can easily recreate the problem. I'm 90% sure it's coming from where the seat post enters the frame. I've got my seat post quick release clamped very tight because I'm heavy (250 lbs) and I was having trouble with my seat post sliding down into the frame. Perhaps I've damaged my seat tube? I'll look into it a little further. I'll be royally PO'ed if I've cracked my frame. Let me know if you get it solved on your end.