In the US it is standard procedure to take the laptop out of the bag. Occasionally it will be checked with a swab for explosives causing a slight (1 to 2 minutes) delay. Outside of the US my experience is that the laptop stays in the bag and gets xrayed along with the other contents.

So in the US, before you get to the security check, put watch, wallet, belt, loose change, phone etc into latop bag and unzip laptop section. Keep boarding pass and photo ID handy. At the machine put laptop into tray and put shoes onto belt or in another tray. Then when you exit the security area pick up laptop, bag, shoes, other stuff and try and juggle it with BP and ID while you find an areas where you can re-assemble yourlself :-).