Despite the different possible themes in his works, one that seems to prevail is desolation in many different ways.
It is evident in The Mask of Red Death, when Prince Prospero and his friends isolate themselves to escape an illness only to find themselves desolate, and ill, by themselves and trapped in the castle.
In House of Usher, desolation is evident in the state of mind of Usher himself, and the deterioration caused by desolation that is evident in the state of the house.
In the Raven, desolation is what is driving the young man to melancholy, as he misses his love, Lenore.
In Annabell Lee there is also the desolation of trying to reach out for his young, dead bride whose sepulchre lays in a kingdom by the sea.
Maelstrom also denotes an aspect of desolation, as the main character remembers his most bitter and saddest moments as he sinks down a maelstrom, to his imminent death (although he survives)
In all, you can see isolation and desolation combine in different shades of sadness, which are a reflection of Poe's own life story. One in which loneliness continued to permeate his psyche.