Creaks and squeaks are a very tricky thing to pin down, the tubing of the frame transmits sound around very well. Have a look at the Sheldon Brown guides for tracking things down, but here is a list of the following things that have caused creaks for me in the past:
1. Dirty seat post, solved by removing, cleaning, greasing and re-assembly
2. Gear cable guides at top of down tube, this can cause a creak with pedal rotation because you are subtly pulling the bars side to side, solved by removing cables from guides and putting a dab of grease on the end of the cables then re-insert
3. Loose headset or stem clamps, just need to be tightened up
4. Saddle rails, solved by tightening up the saddle clamp on to the rails
5. Bottom bracket noise (on a BB30 bike), solved by torquing up the chainset as it had worked loose
6. Noisey wheel rotation if the wheel axle has rubber seals on the outside, solved by putting a drop of light oil on the seals which stops the squeak
7. Creaking clipless pedal, I never did solve this one but it just went away!
Good luck finding your exact problem, it is a bit of a nightmare...
