Left cranks often work loose, and especially on square taper the hole in the (soft aluminium) crank quickly rounds slightly - and then you will never get rid of the creaking.
I had an annoying creaky sort of click on my bike on some recent long rides... never there when I put the bike on the stand, never in testing on short rides from home. Stripped down, serviced, cleaned, re-indexed everything after every ride, and every time this bloody clicking would come back after 50 - 80 miles. Was really begining to fret about it because it's a Campag triple (square taper) ... and it's not cheap to replace bits from that.
On yesterday's Dean 300 km I finally tracked it down, by listening carefully I decided it was in time with the pedal revs - whichever gear I was in. I'd previously checked BB and pedal bearings, so it wasn't that. Finally I was starting to feel the click through the soles of my feet, so decided it pretty much had to be pedals. Thinks - will have to swap the fancy A600 pedals on it for some ordinary M520s when for the next long ride, to see if I'm right. But in the meantime I was facing another 100 noisy miles and it was not a pleasant prospect.
What other moving parts are there apart from the bearings? Well there's the release mechanism....holding my foot at a different angle seemed to cure it, but I couldn't do that and still exert any pressure up hills. Finally when I stopped at the Chepstow control I put a couple of drops of oil on the spring in the release mechanism.... and hey presto the clicking was gone.