The known issues with the S4 have all been covered under warranty and Audi has been really helpful to owners that end up afflicted by these issues.
One of them involves the mass airflow sensor, which did in fact go bad in my car.
It's a $300 part, but it was covered under warranty.
The throttle body boot also ****s out often in S4s, but it's also covered by warranty and isn't that expensive. Audi Performance Racing even had a replacement for it that was more durable and it was under $200.
Other than that, it's been rock solid.