One of the major differences between the movie and Homer's epic poem is that the Iliad ends with the funeral of Hector, whereas the movie goes on to portray other events (e.g., the wooden horse) that do not occur in the Iliad.
Likewise, by the end of the movie, Menelaus, Achilles, and Priam are all killed, whereas all three are alive at the conclusion of the Iliad.
A final major plot difference that is Paris and Helen escape the fall of Troy in the movie, whereas no such thing happens in the Iliad or anywhere else in the mythical tradition. In Homer's Odyssey, Menelaus and Helen are back in Sparta and living as husband and wife. The mythic tradition also has Paris being killed by Philoctetes during the tenth year of the war and before the episode of the wooden horse.
One quick, non-plot point to mention: the role of the gods in the movie is significantly decreased.
Countless other differences between the movie and Homer's epic poem exist, but those are probably numerous enough to fill an epic-sized tome.