I had a very similar problem. It can be a number of things, but it my situation, one of my spark plug leads was faulty... there is a easy way to check the leads with a long screw driver.
I think you place the screw in the socket, and turn the engine over, but make sure the screw drive is near something metal, that way you can see the spark if it is firing. ...then again I could be wrong...
Check the leads before you dig really deep. Start with the cheap items.
A faulty EGR valve can create similar symptoms.
Replace the fuel filter. Check the fuel pressure...
GO BABY GO! 
