Yeah, it could be about 2597 things, but there is a good chance (thanks to ockham's razor, anyone else remember anything from philosophy?) it is something simple.
I had a slight miss that got progressively worse. I was thinking some sort of fuel issue or tune related. So one stock tune with more fuel wot later I was still missing. After checking the plug wires I thought I may have found my problem and I had! I have just replaced the front 3 wires so far (and cleaned the coil pack tops where the plug wire connects) and everything seems great. Now with all 6 new wires and clean coil pack contacts the car runs much smoother. Also, check the spark plugs, sometimes the wire arcs and cracks the porcelain (hairline crack) which will cause it to miss as bad or worse then a bad plug wire. I had this happen earlier this year when I broke the porcelain and didn't know it.
Remember, simply things first!