Thanks!! So looks like taking it to some sort of shop is my next move. The service where they take the car to the glass place and take out the window - was that done under warranty??
Anyway... so here's a story for the morning...
Last day, since I've pretty much established that the rattle isn't coming from the ceiling, I decided to move down and inspect the bottom of the window, to see if the rattle is coming from the panelling around the brake light. After about 10 minutes of looking for the stupid thing, I realized that I drive a Mazda and not a Toyota and my brake light is in the trunk lid... So whatever... Panelling under the glass then! After a bit of further inspection, I consulted a local expert (myself *sniff*) who advised to stuff some towels there and see what happens.
The result... My past 5 drives over all sorts of roads were completely quiet!! So ... This is what I did:
http://i.imgur.com/xZHh6pw.jpg
Now, that still produced an occasional little rattle. So then I did this:
http://i.imgur.com/815WDih.jpg
So currently, I am rattle free. All that's left is to get rid of those towels and see what I can do, to make it not rattle then. I am guessing taking it to service and having them fix it would be a good idea. I can only hope this doesn't run me hundreds of dollars :/ If this is something as simple as just pushing that panelling back into place......