There is a new paper on the genetics of eye color in Europeans that claims to have achieved the highest ever levels of correlation between genes (and other underlying factors such as age, somewhat relevant) and phenotype, reaching 49-52% of accuracy.
Fan Liu et al., Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci. PLoS Genetics 2010. Open access.
The originality of the approach is that they did not just quantify "color" but two parameters: hue and saturation. In both cases (table 3) a SNP (rs12913832A) at the HERC2 gene is most important in eye coloration (44.5 for hue, 48.3 for saturation), followed at a fair distance by age (1.2 for hue, 5.0 for saturation). The rest of the factors (other SNPs, gender) only seem to have minor influence (<0.5%),>
Almost half of the underlying factors of eye color still remain obscure.