- The plot of "ABC" is very similar to the Tom and Jerry short "Busy Buddies". It's worth noting that Tom and Jerry is quite popular in both America and Japan.
- The top screen during "Survivor" is quite reminiscent of survival-horror Light Gun Games such as The House of the Dead. (Or, Resident Evil: Survivor. ) And if you fail the second section, the cutscene has the protagonist out of ammo, with "RELOAD!" flashing on the screen as zombies creep towards him. Said level is also a glorified Shout-Out to another blond-haired-buzzcut hero, complete with freakish "end boss" looking similar to an Octobrain.
- One of the agents is named Agent J.
- One of the game's titular Men In Black wears a fedora and sunglasses.
- What about Khan and the R(h)om(b)ulans?
- An alien invasion thwarted by music? Where have we heard that before?
- Agents are GO!note
- A Pug's Life.
- The "Sk8er Boi" level is actually a reference to The Tuxedo. Especially noticeable when Linda asks Jack "Hey, is your name James?"
- Also a reference to Look Who's Talking. A pregnant woman being driven to a hospital by a taxi driver, being driven by a taxi driver also named James.
- The Divas having double consonants in their names may be a reference to another girl trio.
- There are exactly two animals whom you will help throughout the game. Make a note of their names, if you will.
- The hardest difficulty level is played with the Divas, the only female playable characters, and the difference between it and the second-hardest difficulty is that the note maps are identical but reversed, life meter drains faster, and the note markers are smaller. Recall the old quote: "Ginger Rogers did everything [Fred Astaire] did...backwards and in high heels!"
- "Let's Dance" has "You (do some stuff)!" messages that are reminiscent of old text adventure games.
- Commander Kahn in a Paper-Thin Disguise as "Mr X" might be a reference to The Simpsons episode "The Computer Wore Menace Shoes", in which Homer assumes the online identity of Mr X, whose image consists of a picture of Homer with a black paper bag with a question mark on it over his head.
Shout Out / Elite Beat Agents