The Raja Ampat region of Indonesia is rapidly becoming one of the "hottest" places to dive on the planet. Since it is relatively new to dive tourism, it is facing some of the same problems (anchor damage, destructive fishing practices, etc.) other destinations now manage effectively. The solution is probably an MPA (Marine Protected Area), and great strides are being made to pull together the private, public, and dive operator sectors in this part of the world to ensure the "Four Kings" (English translation of Raja Ampat) keep their crown "coral" jewels intact! For fascinating background, and progress to date:

http://www.coralreefalliance.org/index.php?option=com_content&task=view&id=590&Itemid=246