The Stop command immediately clears the unit's command queue and resets its target.
It does not affect unit states or arrest movement, however: unless under effects of Hold Fire and Hold Position, the unit will immediately resume fighting if enemies are nearby.
Addtionally, Stop doesn't interrupt Commander upgrade or other unit morphs, and cannot prevent an already unleashed salvo weapon (like Thunderbird Lightning) from finishing the salvo.
Stopping airplanes with Idle State set to Land will also cause them to land immediately. This can be used to land Swifts in precise positions that allow them to use their blasters against ground targets without having to waste time on fly-bys.