Misfires
What is a misfire?
An engine misfire happens when you don't get complete combustion of the air/fuel mixture in the cylinder. You really have two types, one that is enough to raise emissions, and worse ones that can actually damage/destroy catalytic converters. With the second type you will get a flashing SES light indicating an active misfire, you should stop/adjust your driving immediately to prevent damage.
What causes a misfire?
You need 3 things for combustion, Air/Fuel/Ignition, below are some common issues that can cause a misfire. Remember, before checking electronics/sensors always check your battery and alternator otherwise you can get false readings.
Air
Dirty air filter
Dirty throttle body
Dirty intake/exhaust valves
Intake/vacuum leaks in seals/hoses/EGR/PCV
Blocked exhaust(cat)
Dirty/failing/bad connection on sensors(MAF/MAP/IAT/TP)
Fuel
Low fuel pressure, pump worn or not getting proper power/clogged filter/leaks/failed regulator
Fuel injectors leaking/failed/bad connections/wiring
Sensors failing or bad power/connections ECT/o2
Ignition
Timing - Check for Pancake Distributor Disease and general Distributor issues. ICM and Sensors - CMP/CKP/KS
Spark plug wires - worn out/loose/cracked
Coils - worn/cracked/connections/power
It's almost never the PCM, rule out everything else first.
Engine condition
Worn cylinders(walls/pistons/rings)
Worn valvetrain pushrods/rockers/springs/rollers/timing chain/sprockets
Valves dirty/worn
Loose/damaged spark plugs