The most noticeable rust spot is located on the driver and passenger side doors, usually at the lowest section of the panel. The actual metal is pretty thick, so you might have a chance at saving the door even if the paint is already bubbling.
The doors are likely to rust due to a design fault. The BMW group decided to compress the sheet metal at the very bottom of the door. The compressed seam was covered with a simple trim peice, sans the sealant. The trim piece would either rot or allow the moisture past it, causing rust to build up and expand.
Make sure to media blast, and treat the inside door as well as the outside. The seams usually rot all the way through.
The most common rust spots on the trunk are located near the mount points for the trunk's bump stop. The surface paint begins to strip after years of opening and closing of the trunk. If the spot is rusted thought, our recommendation is to source new trunk. We also recommend coating the area in rust converter, such as POR-15.
Another spot (not as usual) is located under the mounts for the license plate bulbs. You can temporarily repair the spot with bondo; a proper patch will be hard to pull off for an average hobbyist.
The rust tends to form around the gas door and the supporting frame.
The sunroof panel is prone to rusting due to scratches caused by normal wear and tear. Keep a very close eye on them. Look inside the sunroof panel for signs of rust, and check the rubber seals.
In most cases (especially in lowered cars), the fenders will be bend and cracked around the wheel well. That, combined with years of rock chips and cycles of moisture build-up, makes the fender a very likely target for rust.
Under the carpet, behind the plastic guard that sits on top of the lock hanger.
The tail light seals tend to fail and leak water to the rear corners of the trunk, which causes the trunk to rust from inside out. Thankfully this is a somewhat easy fix as the area is not as restrictive.