Possibilities from a website I found:
Basically, it's one of three things: loss of spark; the air/fuel mixture is too far out of balance to ignite; or loss of compression. Loss of spark includes anything that prevents coil voltage from jumping the electrode gap at the end of the spark plug. Causes include worn, fouled or damaged spark plugs, bad plug wires or even a cracked distributor cap. A weak coil or excessive rotor gas inside a distributor would affect all cylinders, not just a single cylinder.
"Lean misfire" can occur when the air/fuel mixture is too lean (not enough gasoline in the mixture) to burn. This can be caused by a dirty, clogged or inoperative fuel injector; air leaks; or low fuel pressure because of a weak pump, restricted filter or leaky pressure regulator. Low fuel pressure would affect all cylinders rather than an individual cylinder, as would most air leaks. A leaky EGR valve can also have the same effect as an air leak.
Loss of compression means the cylinder loses most of its air/fuel mixture before it can be ignited. The most likely causes here are a leaky (burned) exhaust valve or a blown head gasket. If two adjacent cylinders are misfiring, it's likely the head gasket between them has failed. Also, if an engine is overheating or losing coolant, it's likely the head gasket is the culprit.
Intermittent misfires are the worst kind to diagnose because the misfire comes and goes depending on engine load or operating conditions. They seem to occur for no apparent reason. The engine may only misfire and run rough when cold but then smooth out as it warms up. Or, it may start and idle fine but then misfire or hesitate when it comes under load.
