What percentage of the world population is born with eyes of two different colors (e.g., one brown eye and one green eye)?

Multicolored eyes are fairly rare, usually benign & frequently genetic in origin, occurring in maybe 1 percent of the population.

chacha.com

Congenital heterochromia iridis is said to have an incidence of 6 out of every 1000, which is a percentage of 0.6%. However, a majority of these cases are hardly noticeable and the statistics do not seem to differentiate between "complete heterochromia" where one iris is a different color from the other and "partial heterochromia" where the iris of one eye is two or more different colors. Thus, the incidence is likely significantly lower than 0.6%.

http://www.medicinenet.com/heterochromia_iridis/page2.htm