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http://www.cityseahorse.com/pdf/Raja-Ampat-Cover-Article-Xray6.pdf, by Deb Fugitt
Deb has been diving Raja Ampat since 1999 and is quite well-informed about the destination. This PDF, while highlighting a different boat and tour specifics (from the trip I took), makes a nice reference.
http://www.nature.org/wherewework/asiapacific/indonesia/features/art9103.html
A virtual postcard from Duncan Neville after one of the first serious fish surveys of the region in January 2003 with the Nature Conservancy. A snippet of his observations includes the following: "Over the course of our 22 days at sea we saw amazing things. There were three dive teams - the documentary filmmakers and two groups of scientists that studied hard corals and fish. The fish counting team was led by Dr. Gerald (Gerry) Allen from the Western Australian Museum, a renowned expert on coral reef fishes who holds the world record at Raja Ampat for the number of species seen in a one-hour dive – 283. With three dives a day, almost every time a team came up it was mind-blowing. By the end of the trip the teams had found 828 species of fish, bringing the known total for Raja Ampat to 1,065 species, among the highest diversity in the world. And Gerry got a new personal record of 284 species on one dive, which is about one every five seconds! The coral team found 465 different corals. That means at least 505 species have been found in Raja Ampat, which is well over half of all known coral species. That's incredible! The Conservancy's Asia Pacific Coastal Marine Program Director, Dr. Rod Salm, thinks that the waters surrounding the islands can also serve as a source of fish and coral larvae to replenish reefs to the west and north (even as far away as Japan) which have been damaged by blast fishing."
