Why does our eyes got wet when we feel emotional or whenever we are hurt?
The lacrimal gland, the major source for tear production, is situated just above the eye. It sends it's secretions to the eye via the lacrimal duct. Tears secreted collect in the conjunctiva of the upper lid. There is also a nasolacrimal duct which drains the tears from the eye into the nasal cavity. Hence the sniffles when we cry.

How is it controlled? The lacrimal nucleus in the brain is the major source for innervating the lacrimal gland, is a subnucleus of the superior salivary nucleus in the tegmentum of the pons (part of the brain stem). The lacrimal nucleus is connected to the lacrimal gland by the facial nerve (more specifically the greater petrosal nerve). This is parasympathetic (meaning it is part of the autonomic nervous sytem) and the neurotransmitter transmitting the signal from nerve to gland is acetylcholine (the receptor is muscarinic subtype of the cholinergic... though strangely wikipedia says nicotinic subtype is involved as well, but maybe this is simply poorly worded and is just refering to the ganglia stopover between pre/post ganglionic parasympathetic neurons), this information helps explain how some drugs affect lacrimation (tearing up).

Taken from source (1) [I do not know how reliable this website is]: How is the lacrimal nucleus told to start lacrimation? The lacrimal nucleus receives projections from the autonomic nervous system as well as from various brain structures, including the frontal lobe, globus pallidus, thalamus, and hypothalamus. The projections from the frontal lobe are thought to be important in human psychic lacrimation (crying because of emotions). 

What I know: Another brain area called the limbic system is involved in production of basic emotional drives, such as anger, fear, etc. The limbic system [in the case of sympathetic nervous system it would be the hypothalamus specifically, but this is irrelevant here since parasympathetic nerves cause lacrimation] also has a degree of control over the autonomic system. As I under stand it, the frontal lobe usually inhibits the limbic system.

Again from source (1): While humans across the world produce psychic tears in response to both positive and negative emotions, and while similar emotions have been identified in other animal species, no reports exist of other animals showing psychic lacrimation.

according to wiki (3): Compared to tearing for physical reasons,  tears for emotional reasons have s different chemical composition. They are composed of more protein-based hormones, such as prolactin, adrenocorticotropic, and leucine enkephalin (a natural pain killer), which is suggested to be the mechanism behind the experience of crying from emotion making an individual feel better.

sources:

(1) http://carta.anthropogeny.org/moca/topics/lacrimation-tearing

(2) http://en.wikipedia.org/wiki/Lacrimal_gland#Innervation

(3) http://en.wikipedia.org/wiki/Tears