Weren't milk and tangerines gifts used to bribe Charon, the "grim" ferrymen who transported dead souls into Hades?

I agree with the above posts as far as where the references originate, but I think the song is more specific.

Verse 1: This is about a prison warden who doesn't believe in the penal system.

Verse 2: This is about a priest who doesn't believe in god (or that men have souls).

Verse 3: I'm not sure about this one. I think its about a politician (maybe the POTUS) who doesn't believe in government. I think the "short, brutish mean" line is a reference to the Leviathan, and social contract philosophy in general. There, Hobbes says that in the absence of government man would wage war against every other man (i.e. anarchy) and life would be solitary, poor, nasty, brutish, and short. So if the verse is about government, then the cemetery could be Arlington cemetery (or another military cemetery), and the proprietor would be the head of the military, i.e. the President. Its a stretch, but the verse isn't as clear as the other two.

Verse 1. In "The Human Zoo," by Desmond Morris, he states that humans are not biologically ready to live in an urban environment. And just like animals who are confined in cages, this is detrimental for us socially, causing us undo stress and thus leading to erratic behavior - sociopathic, psychotic, anti-social and violent.

Verse 2. The sacrametal post appears to signify a Church or some place of worship or reverence. The "mean machine" likely refers to René Descartes' philosophical deduction that animals are merely machines, automata with no fee will, but that human beings are more than this because they are said to have a soul and are thus capable of free choice (this is the dualism of mind and body). Thus, the "ghost" is describing the human soul.

Verse 3. In Thomas Hobbes' Leviathan, he describes the natural state or "the life of man, solitary, poore, nasty, brutish, and short." The narrator states that he "plied the grim proprietor with milk and tangerines" which could be metaphorical for something else but it sounds like he is either prolonging his life and/or making his own condition more bearable in some way.

In each verse the storyteller asks a question. Verse 1 he is talking to the "zookeeper" who isn't really different from those at the zoo, hence the response:"don't you know us animals need somethin to do[?]" Verse 2 the "kid" who spilled his wine is asked "aint it funny that machines need a ghost[?]" It's not always the case, but accidentally spilling the wine can superstitiously be thought to bring about good luck or fortune. Perhaps in the verse it represents the kid's prayer to the holiest host (God). In the final verse, the singer asks the "grim proprietor," "so you're short but are you brutish and mean[?]" and the response of course is:

"Hey, I can't deny it, but I won't say anything...unless you ask it right"

For the 1st verse this sounds like the retort "yeah, of course we're just animals, but nobody will find out unless they are actually ready to look for and accept the honest answer it when its revealed." For verse 2 the reply means "yeah, it is a funny and untrue idea that animals(humans) need or have a soul, but nobody will know unless they seek the objective answer." And for verse 3 the response is "yes obviously I am brutish and mean, but people can believe otherwise unless they are ready to accept the reality that I am (that life is)."

Conclusion: Biologically, philosophically, and socially human beings are merey animals - intelligent animals - but animals nonetheless. Yet there is a pervasive denial and so-called belief that they have immortal souls, among so many of us.

***(By the way, Susu.exp's description below is very well done)

I think this song is about God; specifically, why isn't he communicating with us or revealing himself. It's like someone with all the answers to our problems or questions won't deny what you're asking, but won't intervene and make things easier. Also, to "ask it right" alludes to someone praying. Maybe the prayer was answered, maybe it wasn't.

The first verse references Desmond Morris, ethologist and author of "The human zoo", "The human animal" and (best known) "The naked ape". He actually had the same doctoral advisor as Richard Dawkins.
The second verse refers to René Descartes and his book "De homine". Descartes notes that humans are machines, but (that´s where cartesian dualism comes from) ascribes a soul to them. This he argues allows humans to act according to reason, rather than according to "the disposition of their organs", as animals do. This dualist view was parodied as a "ghost in the machine view" by Gilbert Ryle.
Finally the 3rd verse references Hobbes, whose famous dictum from the Leviathan that human life is "solitary, poor, nasty, brutish, and short" is quoted in a slightly altered fashion.
Again this comes from a passage that deals with the nature of man, in this case describing the natural state of humans a a war of everybody against everybody.

So in each of the verses a particular view of the nature of man is presented and questioned. How you relate to these views is a matter of what questions you ask (in sequence: biological, metaphysical and social ones). IMHO the song comes down to stating that there is no singular human nature, but there are distinct human natures, depending on the side from which you look.