First, I avoid the scanners at all costs....analyzing which lines are using metal detectors and which lines are using either x-ray (blue and black machines) or back scatter (the glass tube that rotates and has an L3 logo). Sometimes you just can't avoid them, and if it's the x-ray I choose the opt out to avoid the unproven rays they bombard you with. I may sometimes accept the less dangerous back-scatter machines if the line is long.
If I'm not going through either scanner...and only going through the standard metal detector, then I never empty my pockets ever, regardless of what they are saying to us, except for anything metal. I take off my watch, my cell phone, my metal money clip, remove spare change and a small business card holder that has a spare car key. I put them all in a ziplock bag long before I get to security. That zip lock bag goes into another bag zipped up.
Cash, contact lens case, passport or other ID and various other paperwork stay in my pockets, only metal is removed. Never have a problem.
If I end up being forced into the back scatter scanners (I always opt out of the x-rays), and have some notice, I remove those items from my pockets and hold above my head clearly in view. I never, ever leave my cash, documents and ID anywhere except directly on my person at all times. I'm shocked at the people I see drop cash, wallets, ID's etc, directly into bins in open view. Crazy.
Sometimes they switch you into the scanners at the last second and I still have some non-metal items in pockets. If I don't opt-out (for back scatter), I take the scan, wait for them to ask about what's in my pocket, show it to them, and move on.
Just FYI, I also never ever take out my liquids and place into the bin. Ever. I always have them laid on top of everything in the bag, so it's clearly seen on the xray. I've never had them open the bag for that, and even when they open the bag for something else (usually some wiring or electronics) they completely ignor the plastic bag with liquids. Sometimes they re-run the bag and still leave the plastic bag of liquids inside.
There is truly no logic to the TSA.