I completely agree that there are weird cases of stuff going wrong.
Stuff that's wierd, or very uncommon, etc.

Cleaning cowl drains is not one of those things.  Cowl drains are
common, on many different makes, and have the same problems across all
those makes.  Gunk builds up in the drains, blocking them.  Water
fills up the cowl tray, then finally spills into the car.

Same with sunroof drains.  Plenty of BMW owners have the same
complaint.  :)

E.P.

Some VAG products seem to have problems with water intrusion.  Passat B5/5.5 had a poor design of the cowl drains/pollen filter seal, which would allow water to accumulate in area between engine compartment and passenger compartment, and then flood passenger compartment.  Lowest point (and easily flooded) was comfort control module in floor pan, electronics for locks, etc.

Same model had problems with sunroom drains clogging, which could flood passenger compartment (front or rear) and sometimes leak into headliners on pillars.  

When I read the OP's' first post, it sounded like he was posting about water flooding into cowl area, which I have read of before with this model.  See this post:

I have the same problem with my Audi A6. In my case, the water allegedly went through the vacuum tube to the brake booster (how H2O can enter a vacuum is beyond me) and got into the engine. Net effect, engine is gone.

The car is under warranty and is still under the audi maintenance program. Despite this, Audi is claiming that the damage is not covered under warranty. Estimated repair bill: over $13,000!

I'd be curious to know if others have experienced this problem with Audis. The service manage acknowledged that Audi has known about this problem for some time. I personally think Audi is trying to avoid a recall and class action suit.

To those of you with Audis, the lesson is to remove the battery and check the drain holes. Or have your dealer do it (as they should).

http://www.theautobahn.com/forum/archive/index.php/t-12789.html

 Well to defend the OP some seal defects just happen.
 I think a new VW EOS, yeah I know that it is not an Audi, but this EOS had water POURING in at the car wash.  The techs finally fixed the problem by carefully lubricating this seal with VW's special lube.  Again it is a "maintenance item that was not done from the factory!!
 http://forums.vwvortex.com/zerothread?id=3087297

 Proper maintenance is quite important to catch small problems before they become large ones.
 This is a horror story that hopefully wakes EVERYONE up to check the minor things.

 Is there some list with all of the "uncommon" things to address that will hopefully save one from large headaches?

 --
 later,
 dave
 (One out of many daves)
 1997 Red A4 1.8tq auto

   "Ed Pirrero" <gcmschemist@gmail.com> wrote in message news:138903b4-9915-45a2-940c-d59fbfb498e7@v67g2000hse.googlegroups.com...
   On Jan 11, 2:31 pm, Booker <kitra_b_boo...@yahoo.com> wrote:
   > On Jan 11, 7:52 am, Dano58 <dan.dibi...@gmail.com> wrote:
   >
   >
   >
   >
   >
   > > On Jan 10, 1:57 pm, Booker <kitra_b_boo...@yahoo.com> wrote:
   >
   > > > My 2002AudiA-6 3.0 took in a TON of water in a couple severe rain/
   > > > wind storms this past summer 2007. I have had NOTHING BUT PROBLEMS
   > > > with it since. My brake (re-call taken care of) booster was full of
   > > > water and the brakes FROZE on the road on a trip. Prior to that I've
   > > > been going around with a mis fire in the cylinder (per my local
   > > > mechanic) to the point it misfires so bad it is undriveable. After
   > > > the brake deal and after they said my problem was I needed new tires
   > > > (which I now have) mycheckenginelightis on again (less than a
   > > > week) from the 2nd. tow intoAudi. My belief after much research is
   > > > that it is catalytic converter issues. Possibly from WATER as I cannot
   > > > stress to you enough HOW MUCH water this car took in - bothengineand
   > > > interior of car. I have YET to getAudito direct themselves to the
   > > > fact that ALL the problems I have had with the car is since it took in
   > > > droves of water. With the amount of money $$$$ this car has cost me
   > > > I'm quite upset not to mention it is my only source of transportation
   > > > and since summer of 2007 it is not driveable more than it is!!!
   >
   > > Yeah, I'm with Pete, I'm not exactly sure what your issue is - you got
   > > the car flooded, so that'sAudi'sfault?
   >
   > > Dan D
   > > '04 A4 1.8Tq MT-6
   > > Central NJ USA
   >
   > SO YOU ALL TELL ME? A CAR - ANY CAR - CAN'T BE EXPOSED TO RAIN?

   Not one person has said that.  I know you want to blame Audi, but
   really, the problem ultimately is YOUR fault.

   Not Audi's.

   E.P.