I'm reviving this as I've recently solved the window, armrest and the dash rattle/squeak in the E90M3.
1. windows - the dealership will use 1Z's gummi pflege, which works for a while, but I use Krytox from DuPont, doesn't take much to massage into the seals that are on the door itself and lasts through ultimate cold and heat.
2. Armrest rattle was the button that locks the rest, it needed some krytox on the areas where it rests inside the mechanism near the spring
3. Dash rattle between the mid vents and the HVAC controls. Pry the middle vent section out from the right side and the left side near the "start/stop" button gently with plastic door remover pry bars. No need to disconnect the wires. You'll see the ridge on the HVAC section where the center piece rests, it needs a little krytox on a q-tip and go all the way across. While you've got this panel removed, place felt behind the HVAC unit so when it slides back into the dash, it isn't plastic on plastic.
Hope this helps, sorry no photos yet.
2002 E39 M5 / TiAg / Tubi Rumore / E60 SSK / Blanton 3.45:1 7 disc 40/100% locking diff / NCS Coding / Colby Alcantara / StrongStrut STB