When you really think about how an engine works, about all of the tiny events that have to happen inside at just the right time, and to just the right degree, it's kind of amazing that they run at all. And it's not as though we're in complete control of those events, either: Air and pressure waves can only move at a certain speed, flames only expand so quickly, and fuel and air only combine in a certain ratio. But somehow, automotive engineers manage to get everything dancing together in unison to make for a smooth-running machine -- and we rarely even think about it. At least, we don't until the day the machine ceases to run so smoothly.
Ultimately, any kind of rough running is de facto evidence of some kind of misfire -- if there were no misfire, the engine wouldn't run roughly. Misfires come in two varieties: dead cylinders, with no fuel ignition or power production -- and half-dead cylinders, where the fuel ignites, but doesn't burn right. Obviously, a half-dead cylinder isn't far from going completely dead, and it may do so intermittently. Misfires can be single-cylinder or multiple; single-cylinder misfires are usually easy to track down, since there are only so many things that can go wrong with just one cylinder. Multiple or random misfires mean there's an issue with something that affects the entire engine. Engines have traditionally needed three things to run: air, fuel and spark. Now, add a fifth: computers and sensors. Diagnosis starts with figuring out which of these is the problem.
Fuel delivery problems are usually the easiest to diagnose, but they're the least likely to affect a vehicle at idle alone. A deficit of fuel caused by a bad pump, clogged fuel filters or clogged or malfunctioning injectors will almost always trigger a diagnostic code in any modern car; you can check them using the scanner at any local auto parts store. A fuel pressure loss, or failure of fuel delivery in the case of bad injectors, will throw a "lean condition" code, but the codes that go along with it will tell the tale. If you get a "multiple" or "random" misfire code, you'll probably also get one for the fuel pump, filter or pressure regulator. And even if you don't, it's probably one of the three. Single-cylinder -- even several single-cylinder -- misfire codes usually indicate a bad or clogged injector. However, as stated, fuel-delivery problems are far more likely to cause misfire at high rpm than at idle.
Too much air in the system will also trigger a "lean" code in the engine, but may do so in complete absence of any other. Excess air going into the engine certainly can cause a rough idle that smooths out with an increase in rpm. Vacuum leaks from cracked, split or disconnected vacuum lines are a classic example of just this. However, modern vehicles typically use "idle air control valves" that meter air into the engine at idle, and exhaust gas recirculation valves that feed some exhaust gas into the intake for better fuel economy. Either an IAC or an EGR stuck in the open position will act like a massive vacuum leak; but you should see diagnostic codes for both, and this is fairly rare. More common are valves gummed up with carbon, dirt and oil, which restrict airflow into the engine. You shouldn't notice a bad EGR at idle, but a clogged IAC or IAC channels will choke your engine to death at idle. If this is the case, you'll see multiple or random misfire and "rich" condition codes, along with a weak, fluctuating idle.
Any failure in the ignition system or electronics will cause a rough idle, but the problem will probably get noticeably worse with an increase in rpm. Ignition control modules, coils, plug wires and spark plugs are all candidates; any of them can throw one or several single-cylinder misfire codes, but only the ignition control module and potentially the coil -- if you only have one -- will cause random misfires. All of your engine's sensors are critical, but the likely suspects in a bad idle scenario are the crankshaft and camshaft position sensors, throttle position sensor, manifold air pressure sensor and intake air temperature sensor. The others can cause multiple misfires at idle, but the computer can usually to some extent compensate for the loss or malfunction of any one of them. Vehicles that use the above-mentioned sensors completely depend on them at all times, and anything with "position" in the name can affect your engine at any rpm. A bad computer is always a possibility, though a pretty remote one given all the others.
Hardware failures inside the engine can also cause rough idle problems and misfires. Anything higher than the crankshaft itself is a likely culprit, but that doesn't mean the bearings or crankshaft itself aren't. Most of the time, hardware problems resulting in a rough idle will go back to the valvetrain: the camshaft or shafts, timing belt or chain, the rocker arms and lifters, or the valves, valvesprings or retainers. If anything at all breaks or goes wrong in this system, you can count on at least one consistently misfiring cylinder -- or a random-multiple, in the case of the cam, belt or chain. Blown gaskets, in particular head gaskets, are another possibility; so are intake manifold gaskets. Both will generally cause misfires either because of vacuum leaks or because they allow coolant into the cylinders. Head-gasket failures, usually the result of a heat-warped block or cylinder head, will also vent combustion pressure, and cause one or multiple misfires. Try sniffing your exhaust; coolant smell and oil smoke are never good signs. The list could go on forever in this category; pretty much any kind of hardware failure will interrupt the delicate mechanical dance in your engine. Just hope it's the crank sensor, and start from there.
