Good morning people, not sure if this has been posted before and if it was I’m sorry for reposting it. 
I recently had this problem that was driving me crazy, cracking or knocking noise coming from the sunroof on both driving and passenger side. It started only when the sunroof was completely closed but then I started to hear it when slightly open too. Done a bit of research and heard that it might be the lack of lubrification so a bit of grease will sort that. Bought a tube of spray, lithium based grease and applied it thoroughly inside the canal where the moving parts slide forward and backward. That sorted the problem slightly but the noise was still there. So I decide to do it properly, I took the glass, sunroof off, it holds in 6 screws, 3 on each side, when you open the sunroof you can actually see the holes through the plastic cover, easy to remove, take them all off and then lift the sunroof and remove it, I done it by myself as no one to help but more hands easier the job. For this second lube I used lithium based grease rather than spray because it’s thicker and I believe it does the job better. I greased everything where moving parts are taking place, inside the canal, forwards, backwards, up and down, just open and close the sunroof without the glass on and you’ll see where parts are going in and out and make sure you don’t miss anything, there are a few small places easy to miss especially at the rear of the roof, the two hinges that slide down I believe they were responsible for the knocking. Once you really greased everything just play with the system a bit by opening and closing it few times to make sure the grease covers everything, then check for excess and wipe it down, when I greased, I covered everything in grease, there was a lot of grease excess but that was not a problem to clean at all, easy job. Once you done that give it another round of movement and then finish up by installing the glass of the sunroof back, easy to put back especially if you put the hinges in the close position and then place the glass on top as if the complete sunroof would be closed. Then do some small adjustments to be able to put the 3 a side screws back in place. When you tighten them don’t do it to hard as you’ll still need to adjust the sunroof to make it level with the other parts, just check from the outside to make sure it’s level with the windscreen, doors and the rear of the roof top, slightly lift or push the cover until it perfect and then you can tighten the screw. The sunroof will not close and it will open on its own if the front of the sunroof it’s to low when put back so just lift the front from inside and adjust the screw a bit higher. It’s important you adjust and make it spot on otherwise you might get water ingress. Once all installed again open and close it just to make sure everything is ok and works as it should, then go for a drive and enjoy the peace. It worked absolutely fine for me and there isn’t any noise anymore. It’s not that it’s cheap build but it’s more important we always keep the moving parts lubricated at all times and that goes everywhere around the car. Hope this will help anyone with those horrible noises. Cheers

The correct grease (must be tears from a Unicorn) is VAG part number: G 000 450 02 (£50 GBP) for 90g.

Yes of course, that’s what they say but I’m sure lithium based grease, recommended alternative is as good as that and it only costs £15.