There are many things that can cause squeeks and creaks when you pedal. Start with a systematic look at the various potential causes. Go to:
http://www.parktool.com/repair_help/...queaking.shtml for starters.
I had similar problems that drove me nuts for months. I finally found that it was a very slightly loose pedal that when tightened, solved the problem. I checked them before, but must have overlooked it and went on to other things to tighten.
Check cleats, pedals, bottom bracket, chainrings, chain, derailleurs, seatpost, handlebars for starters. This is a start on a complete list of these things to check. Good luck!