A few days ago I went in to have Toyota flash the brake software, and I also mentioned an annoying rattle coming from the passenger side of the car. The check-in guy showed no surprise at this. In a few minutes a tech came to ask me to ride and narrow down where it was coming from. We drove a few blocks on Santa Fe's typically bad streets, and I pointed it out when it occurred--he heard it. I said my best guess was the door pillar right behind the front passenger door (B pillar). Awhile later he came back, said he had done the software update, and thought he had found the rattle. We drove around again--no rattle. I asked what he did, he said he removed the interior panel (around he seat-belt slide) and looked for wear points, but did not find any marks. He put it back and it stopped rattling. Now I know that problems that go away without a definite fix will come back, so I've waited a few days of in-town driving before posting--so far, so good. He also observed that the coin holder in the cup holder inside the console box rattled, and he had to put a hand on it to quiet it. I knew this, and told him I needed to put something around it to prevent that. This is the coin holder: http://www.amazon.com/dp/product/B000CRO4IK?tag=priuschatcom-20 It is a bit smaller than the cup holder, so I put three soft, clear plastic bumpers around the top--problem solved. One could use stick-on gray foam insulation around it, which would also prevent the occasional coin from being dropped into the cup holder.
Glad you got that rattle taken care of, I have one on the passengers side as well and I thought it might be in that area. I took plastic panels off and removed the seat belt slider and drove around that way to check it, unfortunately that wasn't my rattle.
One definite one Ive fond and it is the passenger air vent and it is really bad. It is so confirmed. Apparently the front plate is super tight but it is the back vent plate that vibrates at certain temp and road vibration to cause it to happen. Once it starts it won't stop for the whole journey and it is extermely loud and annoying.