Hard to diagnose squeaking I am in an ongoing battle to try to get a squeak to go away.  Here is what I know (sorry for the length):

1) The sound is a very loud squeaking (chalk on the board) that, at its worst, persists throughout the entire revolution of the crank.  It seems to be coming from the crank/chainring/BB area, but I would not bet my life on it.

2) I think that it is likely from that area, because its periodicity seems to be linked to the crank speed, not the rear wheel speed (i.e. it sounds the same for all gears in the back, there is only one front chainring).

3) I cannot replicate this sound when the bike is in a stand, it needs to have some (not much at all) resistance.

4) I have tried pedaling with one leg at a time (hard with flat pedals) and it seems to occur for both sides.

5) When it gets really bad, nothing with shut it up while riding.  But, when it is just starting to make noise, back pedaling several revolutions will quiet it down for a minute or so.

6) It seems to be quieter in the morning than evening.  Could just be my imagination, or temperature differences.

7) The sound totally goes away when I clean and lubricate the chain, only to return about 15 minutes into the next ride.

8) Fed up, I replaces the chain, cassette, and chainring a couple weeks ago, but the sound persisted. 

9) It shifts great.

So, I have a hard time believing that it is the pedals or bottom bracket given point 7.  I thought it may be some weird compatibility with the chain and chainring, but it shouldn't be.  I currently have a Nashbar 9 speed chain and a Vuelta 42t chainring (says it is compatible with 7-10 speeds).  The old setup with the same noise was a Shimano 9 speed chain with Surly fixed gear chainring.  The rear derailleur is 4-5 years old.  I thought that there could be some issue with chain tensioning, but I can't really see that either. 

I think I've provided everything that I know about it, but let me know if anything was too vague.  Thanks.
One thing you haven't mentioned: when does the noise occur relative to crank position? Does it make the noise through the entire revolution of the crank arm? Is the noise loudest at a certain point in the crank revolution (say 2 o'clock)? I had a customer come in one time with a sound they absolutely could not get rid of and they went through most of the steps you mentioned. Turned out is was one of the chainring bolts. A little grease on the threads and the problem was gone. It was a ridiculously easy fix for a ridiculously maddening problem!! May not fix your problem but it only takes a couple of minutes to try this solution. You should make sure that all threaded surfaces have grease or anti-seize compound on them. Bare metal threading into bare metal is no-no as it leads to annoying noises, bolts coming loose or bolts seizing/corroding. Good luck!