One very strong overall theme is that of tradition. The "Usher" family is a symbol in itself. Over and over in the story, the narrator mentions how long Ushers have lived in the house, aptly named "The House OF Usher"--not of Smith, Jones, etc. The narrator also mentions multiple times that Roderick and his sister are the last of the Ushers. Once they die out, it stands to reason that the House can no longer exist. They are connected...remember how Roderick and Madeline are feeling ill? As their mental and physical health declines, the house itself "feels" ill and displays it in the hairline cracks of the foundation, the overgrown weeds, the darkness that has overtaken it. The Ushers and the house are one being...and have been for many years...tradition. Once the Ushers die, the house also crumbles and is swallowed by the ground on which it has stood for years and years.
Themes? Take your pick, you got the House being the narrorator's mind, Vampirism, Incest, and others. I tend to believe that the story tells of the narrorator's declining mind. It tells of dark thoughts in head and eventually his mind "collapses" meaning he's gone completely mental. My favorite quote to "prove" this theory is "...while I hesitated not to acknowledge how familiar was all this-I still wondered to find how unfamiliar were the fancies which ordinary images were stirring up." I'd say we could all relate in a way, for what is the most familiar place, and at the same time, the most unfamiliar place? I'd say our own minds.