Could be a combination of things causing an engine misfire. But first I'd replace the spark plug wires (if so equipped). Also add some Chevron Techron concentrated fuel additive to the fuel tank. You could try some CRC also to clean carbon from the engine.
http://www.chevron.com/products/prodserv/fuels/additives/concentrate_plus.shtml
http://www.crcindustries.com/auto/content/prod_detail.aspx?PN=05063%2D6&S=N