I've started to notice a "clunk" whenever shifting in 1st and 2nd gears. 3rd and up I don't hear anything, though.
Like you have stated, it occurs pretty much just after full engagement of the clutch has been reached and you begin depressing the accelerator.
I've found the sound to subside as the car is warmed up, too.
After talking to some people and reading a few ST-forum posts elsewhere I am thinking it is one of the following:
A) Drive-train lash (the slack in the drive-train)
B) Something in the engine bay is being hit by the engine when moves due to torque (unlikely)
ST Crew #65
2007 Liquid Gray ST with SAP1
FocusSport CoolFlo Intake, Balance Shaft Delete, TruBendz 2.5" SS w/ Cat, FRPP Performance Springs