Mental illness and self-loathing
This poem begins by looking at other characters in this coastal town, dodging the speaker's view of himself. Suddenly, in the fifth stanza, the readers are plunged into his mind and experience his trouble. The speaker's declaration early in the poem that "The season's ill" comes to a head as he describes his "own ill-spirit" and says, "My mind's not right." While others are in cars enjoying each others' company, the speaker notes that the graveyard is just outside. The speaker is alone and observes the way in which others around him are alone.
Isolation
Every character in this poem is isolated in a way, but the speaker's isolation seems particularly brutal. When he sees the mother skunk, he seems in awe of her, as if only a creature that ghastly could shake him out of his bitter loneliness, which does not abate upon seeing others—as he does in the "love-cars." All the human characters in this poem seem to be shriveling somehow, and the speaker's isolation is heightened by a possible mental illness, as implied in the line where he holds his own "ill-spirit" by the throat.
Decay and the passing of time
This poem deals with decay and loss, within a person and within a society. The hermit heiress loses some of her sanity due to age and feels she has lost the status that her position would have guaranteed her in the past. She has to buy her isolation in order to regain some of that feeling. Lowell does not seem to mourn the decay of earlier hierarchical structures, but neither does he look with relief to the millionaires that replace the monarchs, instead making fun of the summer millionaire's clothes.
The summer millionaire has died or gone to another home, and his fate remains ambiguous. The decorator, due to his sexuality, seems destined to spend his life alone. Lowell does not hint at any change coming, and this is part of what causes the speaker anguish: the endlessness of isolation.
In the decorator's shop, items that were once utilitarian, like a fishnet and an awl, are now decorative. This indicates that authenticity is eroding in New England. Like the summer millionaire, these things are flattened out into commercial shells of what they once were.
Social conventions
It is apt for a book that broke the conventions of poetry to challenge the conventions of society, as "Skunk Hour" does. The heiress, who stands for old money, is keenly aware that the aristocracy she was a part of is breaking down. However, her replacement, the millionaire, seems even more preposterous. This movement away from aristocracy is not really progress; the conventions of wealth evolve as wealth changes hands. The decorator, on the other hand, makes almost no money and cannot find the love that he wants. However, he doesn't wish for the breakdown of societal conventions. Instead he wishes he could fit into those conventions, desiring marriage.
The speaker, too, desires conventional love and company; he is envious of the couples in their cars. The arrival of the skunks, however, changes that. He finds that the skunks please and inspire him more than religion does. Maybe he can hammer himself into someone who does not always feel like an outsider. But if he cannot, the skunks indicate that there are other ways for him to find joy.