Is the question about coloration or pigmentation?
Coloration comes from two prime components, the zooxanthellae, which is golden-brown and the pigmentation of the coral itself. Anything that decreases zooxanthellae density, or the density of chlorophyll within the zoox will reveal corals pigments more. Anything that increases the zoox or chlorophyll will darken the coral a bit, but too much will make it appear brown.
As for pigmentation, there are a lot of reasons that have been hypothesized. Most have to do with photo-protection, or internal reflection. However, there are probably a lot of reasons. Not much is actually known though, and there is a ton of debate.
One, really cool, newer idea that has come up is protection against oxidative stress from autotrophy.
Biochimica et Biophysica Acta (BBA) - General Subjects
Volume 1760, Issue 11, November 2006, Pages 1690-1695
Quenching of superoxide radicals by green fluorescent protein
Fadi Bou-Abdallaha, 1, N. Dennis Chasteena, 1, and Michael P. Lesserb,
aDepartment of Chemistry, University of New Hampshire, Durham, NH 03824, USA
bDepartment of Zoology and Center for Marine Biology, University of New Hampshire, Durham, NH 03824, USA
Received 7 June 2006;
revised 18 August 2006;
accepted 21 August 2006.
Available online 25 August 2006.
Abstract
Green fluorescent proteins (GFP) are widely used in vivo molecular markers. These proteins are particularly resistant, and maintain function, under a variety of cellular conditions such as pH extremes and elevated temperatures. Green fluorescent proteins are also abundant in several groups of marine invertebrates including reef-forming corals. While molecular oxygen is required for the post-translational maturation of the protein, mature GFPs are found in corals where hyperoxia and reactive oxygen species (ROS) occur due to the photosynthetic activity of algal symbionts. In vitro spin trapping electron paramagnetic resonance and spectrophotometric assays of superoxide dismutase (SOD)-like enzyme activity show that wild type GFP from the hydromedusa, Aequorea victoria, quenches superoxide radicals (O2 −) and exhibits SOD-like activity by competing with cytochrome c for reaction with O2 −. When exposed to high amounts of O2 − the SOD-like activity and protein structure of GFP are altered without significant changes to the fluorescent properties of the protein. Because of the distribution of fluorescent proteins in both the epithelial and gastrodermal cells of reef-forming corals we propose that GFP, and possibly other fluorescent proteins, can provide supplementary antioxidant protection.