Has the car had a tune up recently, at least spark plugs, spark plug wires (if applicable), and fuel filter been changed? It sounds like it could be a misfire issue which often times are due to the items listed above.
Other things to consider would be the Engine Coolant Temperature (ECT) sensor, Intake Air Temperature (IAT) sensor, and Mass Air Flow (MAF) sensor. Have you checked for diagnostic codes? If no codes are present, doing a real-time datastream and monitoring multiple sensors when the car seems to be running well versus when it stumbles might point you in the right direction.
-Rod