The scene in which Homer is strung up by the fishermen is a reference to the movie Jaws.
Homer's job on the fishing boat, their successful catch, and the subsequent storm (including the monster wave that wrecks the boat) are all reminiscent of the 2000 movie The Perfect Storm. During the scene in the institute, a satellite image is seen on a screen, which the oceanographer (based on Todd Gross from the movie) sitting next to the screen says it's "a perfect storm". The subsequent storm (including the monster wave that wrecks the boat), and the funeral service where Homer and the others are memorialized after (apparently) being lost and killed at sea reflecting what happened in the movie.
During a scene in the institute, the Simpsons walk past a model of SpongeBob SquarePants with a nameplate says "The Science of SpongeBob" beneath. The statue also includes 4 molluscs photos and one of them, appears Patrick Star, the starfish and the first two pictures show a crab and a squid, references to Mr. Krabs and Squidward Tentacles.
According to Homer, the Roman god of the sea is Aquaman.
In the final scene, the logs are taken to Larry Flynt's paper mill to be made into issues of Hustler and Barely Legal magazines.