"Help me! Help me!" was #123 of AFI's 400 Greatest Movie Quotes. But the film's influence extends far beyond a simple quote. The movie's concept, ending and the quote have permeated pop culture.

Here are a few examples.
Beetlejuice (1988)

When humans infest a haunted house, the last resort is a bio-exorcist. Betelgeuse is hiding in the miniature version of the town, and when he tempts a fly into range, he drags the insect beneath the miniature graveyard for lunch. Paraphrasing the movie, Betelgeuse mockingly repeats the immortal quote.

Heart On A Chain (1:7)
Eerie, Indiana
premiered November 3rd, 1991 on NBC

Marshall Teller learns Melanie Monroe has gone to Eerie Cemetery to visit Devon Wilde's grave. The transition to the cemetery scene begins with a shot of spider web before panning to the cemetery. While the camera is on the spider web, you can faintly hear a high-pitched voice crying "Help me! Help me!"
Fly vs. Fly (9:4)
The Simpsons: Treehouse of Horror VIII
premiered October 26, 1997 on Fox

Homer buys a set of teleportation pods at yard sale and it doesn't take Bart long to see potential for mischief. Unfortunately, he miscalculates the results of fusing himself with a fly. Now BartFly must find a way to undo the damage before FlyBart usurps his place in the family.
8 Simple Rules for Buying My Teenage Daughter (4:8)
Family Guy
premiered July 10, 2005 on Fox

In the pre-credit scene, Stewie create a "teleportation pod" and tests them out. At the last moment, he realizes Rupert his teddy bear is in the machine with him, and emerges as a Stewie/teddy bear hybrid.


Zip Your Fly (5:4)
The Grim Adventures Of Billy & Mandy
premiered June 27, 2005 on Cartoon Network

Grim removes a mystical zipper from his robe to get his robe cleaned. Billy discovers its power - it can zip (or unzip) anything. He plays around with it until Mandy takes it from him. The next day at school, she accidentally zips her head to a fly and the fly's head to her body.

Day of the Tentacle (computer game)

A severed tentacle is exposed to nuclear waste, giving it human abilities and dreams of world domination. To defeat the purple menace, the players must use such tools as  the Chron-O-John, a time machine that flushes objects through time. If the characters to try to use the same Chron-O-John simultaneously, the resident scientist warns them "Haven't you seen The Fly?". In unheeded, the characters will arrive in a single combined body.


I, Fly (2:7)
Johnny Bravo
premiered September 3, 1999 on Cartoon Network

Johnny fiddles with Carl's science project. a matter teleportation device and in merged with a fly. FlyJohnny searches for Carl to fix the situation and JohnnyFly takes over Johnny's life without anyone noticing he's a giant fly head on the Bravo body.
Teenage Ninja Mutant Turtles

Although Stockman appears in almost of the various incarnations of TNMT, only in the 1987-1996 animated series did Baxter turn into the fly. Baxter episodes include: Enter:The Fly, Return of the Fly, Bye, Bye, Fly, Son of Return of the Fly II, Landlord of the Flies and Revenge of the Fly

The fly Baxter Stockman also appeared in all five TMNT video games based on the 1987 cartoon.
Emperor's New Groove (2000)

The emperor-turned-llama is wandering in the jungle, growing increasingly nervous. He sees a fly screaming "Help me! Help me!" as it's devoured by a spider. After some munching noises, the fly groans, "Too late."
Charlie and the Chocolate Factory (2005)

Tim Burton puts his own spin on Roald Dahl's book as bad little children meet bad little ends, including the obnoxious Mike Teevee who reduces himself to 6 inches tall. As he is battered in the interactive TV, he cries out those famous words of all miniaturized humans, "Help me! Help me!"
Wallace & Gromit in The Curse of the Were-Rabbit (2005)

An experiment goes horribly wrong and now a scientist is slowly changing. Replace the fly with a bunny, add a little Lon Chaney, a touch of King Kong and a lot of cheese. Welcome to the world of Wallace & Gromit.
Jimmy Neutron
"My Son, the Hamster"
Jimmy Neutron has a familiar "bad thing happen" with a teleportation pod. Now he has the head of his pal's hamster and vice versa.

Dexter's Laboratory
"Sole Brother"
Dexter tries his latest ingenious invention, a teleportational device only to discover Dee-Dee has followed him through. Dee-Dee was annoying to start with and it's even worse when the two fused together.

Spongebob Squarepants
"SquidBob TentaclePants" (4:6) November 4, 2005
Sandy Cheeks invents a matter transporter which sends Spongebob into Squidward Tentacles. Can they be separated before Squidward's big clarinet recital?
 

The Fly is also made reference to in the following movies:
Howling III (1987)
The Exorcist III (1990)
Awakenings (1990)
City Slickers (1991)
Terminator 2: Judgment Day (1991)
Addams Family Values (1993)
Wolf (1994)
Multiplicity (1996)
The First Wives Club (1996)
Doctor Dolittle (1998)
Galaxy Quest (1999)
Nutty Professor II: The Klumps (2000)
Little Nicky (2000)