I have a 3 year old (2004) S4 4.2V8 and have not yet done a cleaner service on the injectors.
Is this part of Audi maintenance or is it up to the owner's discretion?

I just did the service on my '02 Volvo (not covered by a maintenance plan)and the difference is phenomenal. A very noticeable improvement in response. Despite using good fuel and injector "cleaners" from the car parts shops the injectors were still filthy.

Anyone done this service (professionally of on their own?)

Cheers

Just did it on mine..Cleaned the throttle body, injrctors and cleaned everything else in-line. They also added a fuel additive to complete the clean. With a new filter it resulted in better economy. Car feels a bit snappier from a dig. Every 15k is whats recommended. The dealer charged me $233 for the service.