It looks like its squeaking without compressing the suspension? I recently replaced the rear triangle of my AT due to deformed dropouts and it developed some creaking- not quite as bad as yours though. It sounded like it came from the BB and mostly when I cranked on the pedals. I looked for cracks and tightened up everything with no luck. I put on a Roco TST shock a few weeks later and cleaned and greased the links and fittings real well with Park tool grease- the manual recommends some Castrol grease you will probably have to special order. It was better after that but not completely gone. After about a month with the new shock (totally sweet by the way) it has stopped. If it started after you removed your shock I would start there.
I found the problem. So earlier, I wiggled the rear wheel, and it was solid, so I thought the dropouts were fine. Turns out, two of the bolts needed 1/8 of a turn to tighten up, and the noise vanished.
Lesson: tighten all the bolts, even if you don't think you need to.