Thought I'd share my "mystery creaking" repair success story with you. I have a 62cm Trek 5500 with DuraAce that I have been riding for 2 years. Recently, it had developed a horrible creaking noise whenever I would stand up while pedaling. It was quite strange and seemed to be coming from the bottom bracket area. I tightened the crank bolts, the cranks, regreased the stem/handlebar junction, and still was consistantly driven to the brink of insanity on any ride. Oh the creaking. I started to dread hills and power starts simply because I knew the creaking would begin.
It's amazing how a wonderful, high end bike that you cherish and love to ride can be reduced to the biggest pile of crap because of one annoying noise. Anyway, I had started to give up hope. I thought I was going to have to pull the cranks and bb to regrease the threads, but because of my lack of mechanic skillz, I was procrastinating by surfing RBR. Well, i did a search, and the most amazing thing happened! I found the solution.
In a thread in the archives, I found a post where someone (sorry i forget the name) said, "hey, why don't you try tightening the front skewer a little bit." I did this, and miracle of miracles, the creaking has disappeared! My jaw hit the ground when this solution was implemented. I never would have thought that a slightly loose front wheel could cause such a disturbance.
Once again, I can hammer down the road in relative peace and quiet.