Firstly; Yes, I didn't wash the car. Secondly, at least we seem to have gotten to the bottom of the 8V S3 Sunroof problem! That thing has been driving me crazy! I hope anyone with similar issues got insight from this video as to how to find and solve a simple noise issue like this on your car! Just do some googling and see what you can find that might help.

EDIT:
From the comments we've deducted that this sunroof rattle problem is present in most VAG cars
Audi Q7
Audi Q5
Audi Q3
VW Golf 7
VW Tiguan
VW Touareg
Audi A3

Luckily these cars share a lot of parts so if your sunroof has these two screws this rattle fix should work for you too!

Anyway here's the original video I found and it helped me a lot:
   • Fix A3 S3 RS3 Creaking Sunroof in 2 m...