In all of the stories you have mentioned, a main character is alienated by his madness or intelligence.
In "The Black Cat," "William Wilson" and "The Fall of the House of Usher," the main characters are alienated by their madness. In "The Purloined Letter" and "The Gold Bug," the main characters are alienated from others by their superior intellect.
Alienation is a common theme in Poe's work for several reasons. First, Poe knows alienation because of his personal life: he was alienated from parents, then from his adopted family, and ultimately, from his wife, who died so young.
Alienation also seems a necessary component for the author in order to build either suspense or the presence of madness (or both) into Poe's stories so that there are no witnesses and/or no "voices of reason" to sway the evil or dark intent, or predilection to madness, that so many of Poe's characters experience.
It is interesting to note the irony of alienation for Poe: it haunted his waking moments and made his life a misery, however it is also what drove his creative genius, and "flavored" so many stories that remain Poe's greatest bequest to the literary world.
To answer your question in general (each work is considered a separate question), the main characters in each of these stories have a personal torment that they have to resolve but that seems to be taking the best of them. All the main characters are in the verge of insanity or are going to become insane at some point due to a fear, preoccupation, or an obsession that is inherent to them. I can give you an example with black cat. The main character was tremendously disturbed by his cat, Pluto, when in fact before he used to love and take care of it. His isolation came as a result of that personal torment, and not caused by something from the outside. It was less of a choice and more of an impulse caused by insanity.