I have had the problem a couple of times. It is always one of three things:
Loose BB
Loose crank bolts
Loose pedals
Almost always the first and rarely the other two. I run a Ritchey crank on an Ultegra Octalink BB and an Ultegra 6500 on an Ultegra Octalink, my wife's bike has a Specialized OEM crank on some square taper BB and my MTB is running a Bontrager crank on a Race Face Evolve XC ISIS BB. None of these creak at the moment.
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