1999 Audi A4 slugish acceleration

Today my A4 suddenly started to "chug" when accelerating, as if the compression or firing were off. When using the automatic "stick", when I would leave in in lower gear and let it wind out a bit, it wasn't too bad. But accelerating for freeway speeds seemed like a bad idea. The check engine light came on and flashed, and continued flashing. What is the likely problem and would it be worth my while to take it to a dealer to fix or have it worked on by someone else. To date, I have taken it to the deal for all service. These German cars seem very fussy and fixing them is expensive. I am trying to decide in fixing it would be worth while or if I should call it a day and get a new car.