The Japanese fishing boat that rescues the crew is named "Iruka-Koroshi-Maru", or "Dolphin Killer" in Japanese.
The title is a reference to the film "Life Aquatic with Steve Zissou".
The episode contains numerous references to the 2000 blockbuster film "The Perfect Storm", taking place during the time Homer is onboard the fishing vessel and later on when it is capsized by a huge wave.
A scene at an Oceanography institute for the 2007-airing episode shows what "global warming will cause in the next 3 years" by having a display of what looks to be New York City being flooded and many people drowning. 5 years after this episode aired, major flooding in NYC was caused by Super-storm Sandy and the effects were similar to what was shown here.