Remove the emergency metal blade key that is located within the ignition key and place it in the trunk lock keyhole that is located next to the trunk release handle (squat down a bit - you'll see it above the license plate). Turn the key to the left approximately 45 degrees (+/-) and hold it in this position. While holding the key in this position, work the trunk release handle. Let us know if this works.

For illustration, go to the Practical Hints section of your owner's manual, and in that section is a subsection called "unlocking/locking in an emergency" On the online version of the 2006 E Class manual, (link below) it starts on page 426.

http://www.mbusa.com/vcm/MB/DigitalAssets/pdfmb/ownersmanual/2006_e320cdi_e350_e500_e3505004matic_e55amg.pdf

See picture below for image of latch (black rectangular strip directly below star and above license plate area) and the trunk lock keyhole (oval/round area to the left of the latch):