My 2005 VW Passat 1.8 turbo is running very rough (sputtering and shaking while driving). The check engine light has been on for quite a while and this morning it started blinking. What could be wrong?

First make sure that you have plenty of oil. Check the dipstick level asap. If your oil is good, at least you haven't cooked the engine. You could have a huge laundry list of problems. I would get it to a garage as soon as I could. You may have anything from a clogged oil line, to just a bad O2 sensor with a really dirty throttle body and IAC valve. Since you have waited so long with a check engine light, and now it is blinking, I wouldn't drive it anyplace except the nearest auto shop.

I just want to add that be sure you take your car to a certified vw or audi specialist in your area since most joe blow mechanics have no idea what to tell you and most often do not have the proper tools to properly diagnose your car. but a stutering and shudder is most commanly cause by a fuel, air or spark issue in the vw or audis. Try changing your spark plugs if they look blacked and have the mass air flow sensor cleaned it may or may not fix your issue, tho im guessing since the engine light is on its most likely a bad sensor then anything it can also be a bad coil pack since this modal has seperate coil packs for each plug. if your not car savy tho or are not familure with vw's jsut take it to the garage and have them do the work for you and at least you may maybeable to give them a brief idea where to start first and help speed up the diagnosic process.

Thank you so much for taking time to answer my question. I appreciate it.