Well, I think the first clue is when they put their lights on and tell you to pull over, if you don't then they have reason to call in the cavalry and "maintain order and justice in the land" by forcing you to stop, comply, lie face down while they cuff you first and ask questions later.

If you play nice (darn) then they ask the questions politely first and look for "tells" - you know: blood dripping from the trunk, piles of loose cash in the floorboards, a dark complexion (driving while black) - all the "usual suspects'" signs - probable cause. A remarkable percentage of actual criminals are not stone cold liars who are able to cooly answer the questions and act like nothing unusual is going on.