I just had my 90,000 mile service on my 1999 A6 Quattro 2.8 including Timing Belt, water pump, full tune up, etc (cost me $2300!) right before Christmas.

Was away for Christmas and when I got back, I started my car, and the "Check Engine" light was lit and it was idling very rough.

Brought it in and they told me that the Fuel Injector #5 was bad and needed to be replaced. The problem is that I was told that Audi has changed the injectors from 4 hole to 6 hole and the old injectors are not available and cannot be installed on the car. This means I have to buy 6 new injectors. Close to another $1000 worth of work!

This car is just over 2 years old and they obsoleted parts like this? Sounds to me like they had a bad part and replaced with something better, but did not do a recall like they should have.

Anyone else know anything about this?

Take the car to your dealership and claim that it starts very bad when cold. It may be that the injectors are dirty due to bad fuel and a lot of short distance driving/engine not warming up as should be. Service will disassemble and clean the injectors (a 7 hour job I was told).
It's a known problem. A cleaning will keep the injectors in good working order. Oh, BTW, Audi uses a special Chevron Techron cleaner, I think it's the same as we can buy but more concentrated.

Whilst we are at it, after 40,000mls change to synthetic oil (in case you want to keep the car longer), there are seals at the end of the camshafts, they shrink and cause oil leaks. Synthetic oil obviously is better to prevent this.
Check now, it may happen earlier than that! Maybe it's ignored by service, so check! This damage can be "hidden" easily since the leak is small and oil will be caught by the undertray/pan. During the used car check this is one point which should be repaired and at the dealership sales and service are always fighting over this....

Cheers, sorry this won't help you but.....