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Problems that are specific to the C4 body S6 are:

Ignition coils that fail resulting in misfire at higher boost levels.  Very
difficult to track down which coil is the culprit when it happens.

The Power Output Stages (POS - and it really is), which trigger the coils,
also fail.  Typically it is a constant misfire and can easily be diagnosed
at idle by disconnecting the injectors one cylinder at the time until you
find the one doesn't result in a change.  With the POS at least you get one
free fix, assuming the PO hasn't already taken advantage of it.  There are
two POS's with 3 channels each, so one is available to swap with the bad
one.  

Factory coils are approx $100 each.  A POS is probably $150-$200, don't
really know as i haven't priced one lately.  Your car is at the mileage
where if they haven't had a problem yet, they will soon.

There is an alternative fix that is out there now that replaces the factory
coils and POSs with the coils from the 1.8T, which have POSs built in.  Kits
are now available from 034Motorsport and Apikol for around $300+, or you can
roll your own for less.  You won't want to reinstall the coil cover when
going this route as the heat buildup is likely too much for the 1.8T coils
and will result in premature failure.  There are several folks running this
set up now.

If I needed to change my coils right now, I would opt for the original
factory setup.  Yes it is expensive.  But it is a known quantity.  Plus I
don't really care for the kluged look of running sans coil cover.

Another S6 specific problem, like other turbo Audis, will be the intake
hoses.  Usually the Michelin Man hose, which is the one connecting the
cross-over tube to the intercooler, will fail.  Samco makes a replacement
set of silicone hoses which run $350 for all three - turbo to X-over tube,
MM, and intercooler to throttle body.  There have been 2-3 GBs over the last
few years that usually result in a price of about $260-$280 for the set.
Given you have an MTM chip already, it's possible that the original hoses
have already failed due to the higher boost and been replaced with Samcos.

The transmission can develop a whine, or sometimes a ticking, in 1st gear.
The problem is due to galling of 1st gear on the main shaft.  In later
years, like 95.5 models, the mainshaft was replaced with a one that has a
wider 1st gear.  The clicking noise seems to be more prevalent to the
earlier '92 - '94 S4s. My '95 S6 has the whining noise.  I equate it to the
noise of straight cut gears.  Frankly, if you develop that I wouldn't worry
about it.  Mine started at around 50k miles and now have 100k miles on it.
After 50k miles of hard 1st gear launches it hasn't gotten any worse.  I've
tried to break it but it just scoffs me and asks for more.