People come up w/ this question alot...for obvious reasons. For me the answer is VERY easy, it comes down to whether or not you need a manual transmission. Now, since I bought my car new at the end of 2008, the GXP's were just getting on the lots. I test drove a manual GXP, an A6 GXP, and an a GT w/ sport/premium packages. The brakes don't matter to me since you can upgrade that as part of your regular maintenance (I did - see sig) and TBH, unless you're tracking the car the GT brakes are just as good performance wise ON THE STREET. The big deal for me was I simply couldn't justify the extra $10,000 at the time for a manual tranny...the auto GXP didn't blow me away enough vs. the GT so I got over it saved the money and bought the GT.
Now, the delta between used GT and used manual GXP has shrunk some, but not by much, so you gotta ask yourself is it worth the extra cash for a manual tranny...and believe, it IS the manual tranny that makes or breaks the car IMO, there are NO big, 4 door, RWD, reliable, V8 big power sedans out there w/ 6 speed manuals....NONE. Let alone "american" ones.
But for A6 cars, dollar for dollar the GT is the better buy every day of the week and twice on Sundays. You can match stock GXP performance w/ intake/dyno tune if you have a strong GT, take off the cats and/or add HFC's and/or add headers and you'll be slightly quicker than a GXP.
All that being said, if it were a $5,000 difference for the manual tranny and brembo calipers when I bought new I would have paid it, but anything more is too much, and in the used car market it really comes down to preference.
Stock for Stock, A6 to A6, mileage/color/condition all being equal, I would never pay more than $3500 for the GXP over the GT auto...that's more than enough $$$ to surpass it and when you mod the GT it becomes more "YOUR" car anyhow.
Oh and lastly, you mod the GT w/ say intake/headers/tune/brakes - now you got a GT that is faster than the GXP AND GETS BETTER MILEAGE - considerably, so keep that in mind too if it matters.