Akira, in case it hasn't already been mentioned.
The Decline of Western Civilization, if documentaries are allowed to be considered cult films.
Henry - Portrait of a Serial Killer, might be considered a cult film. Don't know if there is an active fan base exactly, but it is a very powerful and polarizing film in how it depicts cinematic violence. I recall Fangoria saying that it was the first film that the MPAA did not give the option of cutting certain scenes to obtain an R rating, it's overall tone was just too dark and disturbing.
Fitzcarraldo.