I had two RS6 customers in my time with Audi: One was reliable enough, save a rattle or two, and the other one needed a new transmission and all of its catalytic converters. Fortunately, the warranty was just short of its expiration date and under 50,000 miles, and the factory picked up the tab. I'd never known a car that needed all of its 'cats replaced, and wasn't poisoned by diesel fuel, rusted out, nor had over 120,000 miles...for whatever reason, the ECU didn't like being replaced (same DTC codes when swapping with a known-good unit), and so that was an absolute rarity in my 5 years of being in a dealership. The transmission issue was unusual for a low-mileage A6-architecture, as well.
Mind you, this was one of the most expensive bills I'd every seen the factory "eat", so Audi took their sweet time inspecting everything. Combine that with parts delays and diagnostic time verging on weeks, so the customer didn't get his car back for 6 weeks. On the other hand, he was away on business for a month, so he wasn't really bothered.
Audi rarely (if ever) sells cars as Certified Pre-Owned that have no basic factory warranty left, and if you do buy someone else's CPO car, the warranty is not transferable to another owner, regardless of the time/mileage left on the existing policy. Audi parts are either surprisingly cheap (there's a number of VW parts) or very expensive; there's a good-sized aftermarket, but don't think "Honda-tuner-brand" prices for a minute. Get to know a good VW/Audi mechanic or German car-specialty shop with low labor rates; the forums usually know of one in a particular area, although if you live in the sticks, it's a must. Remember that RS-series Audis are not cheap to maintain and parts are likely to wear out faster than the normal variant of the car.
My only pet issue with that A6 (1998?-05) and its variants was the way that automatic shifter lever and its bezel rattled and felt shaky when moving it from drive mode to park, et cetera. Some of the A6 interior trim is kind of rattle-y and loose to the touch after a few years. It isn't Toyota/Honda-quality (four years of working at Lexus will certainly change those kinds of expectations). But the chassis dynamics are much, much race-car like, a solid car over the bumps, though sometimes the shocks and struts are going to be leaky after a few years. Brake parts replacements (repair? resurfacing? Hah!) are going to be hideously expensive on the RS-series: Go home and brace yourself with a Valium in preparation before looking at the invoice or getting the call from the shop.
US-bound RS6's had a nicely contrasting leather and suede combo, and can be quite the sleeper car in appearance. Like most factory Audis with 400+ horsepower, they're absolute pussycats to drive at slow speeds; you do not have to worry about it "getting away from you" in a parking lot or when stuck in traffic.
Edit: We had a lot of automatic transmission replacements when I was at Audi, but no more than when I was at Lexus (Honda had their own issues in that department). Ninety percent of the time, Audi tranny failures were the A4's CVT units, with one or two here and there on the other models. Audi customers complained about the FronTrack CVTs with a passion, and the transmissions apparently didn't like them in return. It goes to show that sometimes the customers have a hunch that their cars aren't quite right when it comes to transmissions.