The amount of a black-brown pigment, eumelanin, in the iris is the main determinant of eye color, Morgan Worthy explains (in I Have Known the Eyes Already):
If there is a high enough concentration of eumelanin, the eye will appear brown. If the concentration is very high, the eye will appear black. If the particles of melanin are very small, a light-scattering effect will cause the iris to appear blue (for the same reason that the sky appears blue). Eye color is also determined by the amount of a yellow-red pigment, pheomelanin, in the iris. There are other factors involved, but that is the basic difference between dark eyes and light eyes. If you like, I can give you a recent article (Borteletti et al. 2003) that discusses various other factors that can influence iris color.
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Amount of melanin in the iris is correlated with amount of melanin in the inner ear (Bonnaccorsi 1965) and with amount or distribution of neuromelanin in the central nervous system (Happy and Collins 1972). In terms of the link to motor behavior, it is perhaps significant that neuromelanin can function as a semiconductor (McGinness et al. 1974). Eye color is polygenic and the specific genetic causes are still being sorted out (Zhu et al. 2004). I just use eye color or eye darkness as a marker variable that is external and easily observed. In fact, eye color was used as a marker variable in many of the early studies of genetics.