Crying or tearing, is known scientifically as lacrimation. Although most land mammals have a lacrimation system to keep their eyes moist, humans are the only animal generally accepted to cry emotional tears.
Tears brought about by emotions have a different chemical make up than those for lubrication; emotional tears contain more of the protein-based hormones prolactin, adrenocorticotropic hormone, and leucine enkephalin (a natural painkiller) than basal or reflex tears.
The limbic system is involved in production of basic emotional drives, such as anger, fear, etc. The limbic system, specifically the hypothalamus, also has a degree of control over the autonomic system. The parasympathetic branch of the autonomic system controls the lacrimal glands via the neurotransmitter acetylcholine through both the nicotinic and muscarinic receptors. When these receptors are activated, the lacrimal gland is stimulated to produce tears.
(My Summary of Wikipedia: http://en.wikipedia.org/wiki/Tears)