Originally Posted by Camilo

Removed, cleaned and re-greased pedals. Cleaned and lubed pedal mechanism (Time RXS). Re-tightened cleat bolts on shoes .... also tried my MTB pedals and MTB shoes (which I've been using on another road bike which doesn't creak at all).
Removed, cleaned and applied assembly paste to seat post (Ritchey carbon fiber post) re-lubed and re-torqued seat post clamp.
Removed saddle. Cleaned and greased rail-rail-clamp attachment. Greased and re-torqued rail clamps.
Removed stem and cleaned and applied new assembly paste to steer tube and handlebar and greased and re-torqued stem bolts.
Removed, cleaned and re-torqued all chainwheel bolts
Removed, cleaned and re-torqued cassette
Cleaned and re-lubed chain
Fine tuned rear shifting
Removed the BB again. Re-cleaned and this time I used teflon tape on the bearing cup threads instead of grease. Reassembled and re-torqued.

Any other ideas? I'm kind of at a loss.