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The check engine light on board diagnostics OBD II system is on 1996 and up (cars and light trucks.) The OBD II system monitors the sensors and actuators that run the engine. When one or more actuator or sensor goes out of spec the processor recognizes this and turns on the light. There are many sensors and actuators in these systems that may cause the light to come on. If the light flashes on and off continuously it indicates a serious problem and the vehicle should not be driven, because of the possibility of creating mechanical damage.
In New York State the vehicle will not pass the emmission part of the inspection if the check engine light is on. When the vehicle is inspected the check engine light needs to come on when the key is on and the engine is off, when the engine is then started the check engine light needs to be off. 
When the light is on it needs to be diagnosed and have the problem repaired.  This should be done by an ASE certified technician with an updated scanner.  The problem can be anything from a missing gas cap to a bad sensor or actuator to replacing and reflashing trhe processor. After that is done it needs to be driven for a drive cycle so that the monitors can ready themselves. For a drive cycle to complete the vehicle needs to be driven about 30- 50  miles sometimes less sometimes more to ready enough monitors. For vehicles 1996-2000 you can have up to two monitors not ready when inspected. On vehicles 2001 and newer there can be only one monitor not ready. To have the monitors ready themselves, they need to go through certain conditions. One of these conditions to run some monitors is the ambient outside temperature needs to be above 40 degrees and in certain circumstances be left in a heated garage overnight and then do the drive cycle to make some of the monitors run. NewYork State has a universal drive cycle that seems to work well for most vehicles. 
The universal drive cycle is:
1. The OBDII drive cyle begins with a cold start(coolant temperature below 122 degrees F and the coolant and air temperature sensors with in 11 degrees of each other.
2. The ignition key must not be left on prior to the cold start-otherwise the heated oxygen sensor diagnostic may not run.
* As soon as the engine starts, idle the engine in drive for two and one half m,inutes, with the air conditioning (A/C) and rear defrost turned on, if equipped...
*Turn the A/C and rear defrost off, and accelerate to 55mph under moderate, constant acceleration. Hold at a steady speed of 55mph for 3 minutes.
*Decelerate(coast down) to 20mph without braking (or depressing the clutch for manual transmissions.)
*Accelerate again back to 55 to 60mph.
*Hold at a steady speed of 55 to 60mph for five minutes.
Decelerate (coast down) to s stop with out braking.
The information above is general information and for diagnostics, repairs, and drive cycles specific to your vehicle you will need to see your repair facility.