SOURCE: 2000 VW Jetta VR6 My
You may have a bad coil pack - try moving two of them around and see if the misfire follows the coil pack or stays at the same cylinder. If it follows the coil pack, get a new one. If it stays in the same cylinder, inspect your spark plug wires and make sure the plug is gapped correctly.
SOURCE: 1999 Town Car began running very rough - suddenly.
When cleaning your engine, water/degreaser went down the spark plug ports. Try using a air compressor blow gun to remove the moisture from around the spark plugs and boots. The water was causing the engine to misfire on 3 cylinders at first and as the ports started to evaporate the moisture, the less misfiring was occuring. Dry thouroughly and hopefully coils do not have damage to them. Also check to make sure the boot is making good contact with the spark plug.
SOURCE: 2002 grand am 4 cylinder rough idle and rough running
Check the ignition control module. Sounds like the exact same problem I have had with mine. Took it to the dealership and the were able to tell me right away. The ignition control module is very easy to replace and is located on the top of the valve cover. Hope this helps!
SOURCE: MIL indicates cylinder misfire on 1, 3, and 5
Check for
vacuum leaks on intake manifold,
the air tube between the air filter.
intake manifold vacuum hose.
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clean throttle plate with Berryman carburator cleaner
SEE sample picture HERE
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Also remove carbon built up behind the EGR valve and the EGR passage tube.
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Vacuum leak WILL offset the intended 14.7 to 1 air fuel ratio.
More un-metered air (leaks) will lean out the fuel mixture.
Use small amount of Berryman carb clearer at potential air leak area will help you identify trouble spot.
At idle,just spray and listen for the RPM surge.
The in-rush of carb clearer will increase the RPM on the motor.
Record the problem spot(s) and address it later.
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EGR carbon built up require 2+ hours to clean from start to finish.
You will need a new EGR base gasket before your start.
Locate and remove the EGR valve after the vehicle is cool down.
Carefully record the connector and vacuum line (for older vehicle) location by drawing an easily to follow diagram.
Remove the EGR valve.
Inspect the location of the carbon built-up inside the valve and the EGR passage tube.
SOAK these areas with WD-40 spary.
You will need a small screwdriver,cloth hanger and lot of newspaper and time to get this cleaning done right.
RE-SOAK the carbon and let it sit for over-night will also help.
One the last round,pass a shop vacuum of the EGR valve and the passage pipe.
Install the new EGR gasket and connectors.
Allow the vehicle to warm up outdoor to burn up any remaining WD-40.
Take it for a test drive.
Please rate my answer if it's useful to you.
Cheers,
Mustgo
If it is an overhead cam engine with a rubber timing belt, a broken timing belt 
would be the most likely cause especially if the engine has a lot of miles on it. Most OEMs recommend replacing the OHC timing belt every 60,000 miles for preventative maintenance, but many belts are never changed. Eventually they break, and when they do the engine stops dead in its tracks. And in engines that lack sufficient valve-to-piston clearance as many import engines and some domestic engines do, it also causes extensive damage (bent valves and valvetrain components & sometimes cracked pistons).
Overhead cams can also bind and break if the head warps due to severe overheating, or the cam bearings are starved for lubrication. A cam seizure may occur during a subzero cold start if the oil in the crankcase is too thick and is slow to reach the cam (a good reason for using 5W-20 or 5W-30 for winter driving). High rpm cam failure can occur if the oil level is low or the oil is long overdue for a change.
With high mileage pushrod engines, the timing chain may have broken or slipped. Either type of problem can be diagnosed by doing a compression check and/or removing a valve cover and watching for valve movement when the engine is cranked.
A blown head gasket
may prevent an engine from starting if the engine is a four cylinder with two dead cylinders. But most six or eight cylinder engines will sputter to life and run roughly even with a blown gasket. The gasket can, however, allow coolant to leak into the cylinder and hydrolock the engine.
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