Heart of Darkness
by Joseph Conrad
Symbolism, Imagery, Allegory
This one's practically a freebie: flies have been symbolizing death ever since flies hung around dead bodies (so, forever). Slightly more recently than "forever"—but also a long time ago—the devil got the nickname "Beelzebub," which most people translate as "Lord of the Flies." (We're pretty sure William Golding had read Heart of Darkness.)
In Heart of Darkness, flies notably appear when an agent dies in Chapter One ("In the steady buzz of flies the homeward-bound agent was lying finished and insensible" [1.48]) and when Kurtz dies: "A continuous shower of small flies streamed upon the lamp, upon the cloth, upon our hands and faces" (3.44).