It also could be:

*Spark plug wires out of order

*leaky injector letting air in and messing up the mixture

*leak in intake manifold gasket allowing air in there and screwing up the mixture.

For the latter two, try spraying carb cleaner around the injector ports and the intake manifold where it meets the head while it's running. If it runs better when you spray the stuff, you've found a leak!

Ben