Vibrations can be caused by driveline issues such as failing motor or transmission mounts, or out-of-balance driveshafts. But true engine vibration usually comes down to one thing: cylinder misfire. But the misfire itself is just a symptom of another problem, and that's what you'll likely end up looking for.
The first thing you need to do is find out whether you have a misfire on one or more individual cylinders, a "random multiple misfire" or no misfire at all. The simplest way to do that with any vehicle made since 1996 is to check the diagnostic trouble codes with a generic OBD-II scanner, available for use at most chain auto parts stores. This critical first step, combined with any other codes you may get, will save you a lot of time chasing dead-ends in diagnosis.
Cylinder misfires generally come down to a failure in one of four systems: air supply, fuel supply, ignition and the sensors that control them, or the computer. To much or too little air or fuel, or the lack of an adequate spark, will cause misfire. Again, the diagnostic computer will be your best friend here, since it will tell you if there's a "lean" condition indicating too much air or not enough fuel, or a "rich" condition indicating too much fuel, not enough air or an ignition failure. Most modern vehicles will also self-diagnose a bad sensor or electrical connection, but that isn't 100 percent reliable.
A "random multiple" misfire means there's a failure that affects the entire engine. These are "general" kinds of failures, often something outside the engine itself. "Single cylinder" misfires are much more specific, and often indicate a failure closer to, on or in the engine. There are only so many things on the average engine that only affect only one or two cylinders. If you get no misfire code, it likely means there's some sort of mechanical failure that's caused the rotating assembly to go out of balance.
Problems affecting the entire engine usually go back to the engine's "life support" systems. Those being the fuel supply, air intake system and the electronics or computer systems. A "lean" code with this means the engine is getting either too much air or not enough fuel. Too much air generally comes from a vacuum leak, though a failed or dirty mass airflow sensor will cause it as well. Fuel deficits typically go back to a clogged filter, or bad fuel pump or regulator. "Rich" codes affecting the entire engine generally indicate an ignition or ignition control problem, though air restrictions in the intake -- such as from a clogged filter -- can cause them, too. Many sensor and computer control failures will cause this, including a bad camshaft, crankshaft, MAF or MAP sensor.
Single-cylinder misfires usually come from an ignition failure or a fuel injector problem. Bad spark plugs and plug wires are classic culprits, but you could also be looking at a bad ignition coil. "Coil-on-plug" engines will misfire on a single cylinder if that cylinder's coil goes bad; these failures are usually pretty obvious. However, you could also have a bad coil if you've got two cylinders consistently misfiring. Many engines use a single coil to power two cylinders; so if that coil goes bad, both cylinders will die. In either case, you'll most likely get a "rich condition" diagnostic code as well. A "lean condition" code will most often indicate a bad or clogged fuel injector.
A single-cylinder misfire could also indicate a mechanical failure, like a broken piston ring, blown head gasket or problems with the valvetrain or camshaft. Engines with VTEC-type variable valve timing can throw random-multiple codes if something goes wrong with the system, or if oil pressure is too low to activate it. If you get no misfire at all, it's likely something is out of balance in the rotating assembly and causing the engine to vibrate. A lot of mechanical things could go wrong in the engine and cause this, but most likely it's a bad harmonic balancer. Many engines also have "balance shafts" that reduce engine vibration, performing essentially the same function as a harmonic balancer. If you've got balance shafts, they may be worth looking at on an engine that shakes but doesn't misfire.
