The throttle setting determines the demanded thrust from the engine(s) on the active stage of the craft. The throttle may be set anywhere from 0% (or "closed", meaning that engines are inactive) to 100% (or "open", meaning that engines are producing their highest level of thrust).
The throttle indicator is located to the left of the navball.
The throttle can be controlled with the ⇧ Left Shift and ^ Left Ctrl keys, which will respectively increase and decrease the throttle. When in Intra-Vehicular Activity view, the throttle lever in the cockpit can also be used by clicking and dragging it with the mouse. The X key will immediately cut the throttle (faster than holding down ^ Left Ctrl); conversely the Z key will immediately set the throttle to maximum. When a vessel is first launched from the Launch Pad or Runway, the throttle is initially set to 50%.
Activating non-physical time warp will automatically cut the throttle if no engines are firing. If engines are firing, non-physical time warp cannot be used. Physical time warp may be used, but at the risk of destabilizing the ship due to the loss of calculation accuracy while accelerated.
Liquid engines are controlled directly by the throttle in the most simple way- the higher the throttle, the more thrust they produce and the more fuel they consume. Higher throttle settings also cause the engine to overheat, which can lead to explosions if not caught in time. Some engines, most notably the mainsail, cannot be run at 100% throttle for long periods at all.
Jet engines respond to the throttle, but just like real-life jets they exhibit throttle lag. The thrust they produce will adjust slower than the speed at which the throttle is moved and it will take extra time for them to change their power output to match its new position.
Solid rocket boosters do not respond to the throttle at all; once activated by staging they will instantly produce 100% of their thrust (adjusted by the thrust limiter, only available in the VAB / SPH) and run continuously until their fuel is exhausted.
In Linux, if you are using a joystick to control your throttle, only part of the throttle range may be available depending on where the throttle was set when you started KSP.