One of Peppy's most well known lines, "Never give up. Trust your instincts.", was added because one of the developers, Mitsuhiro Takano, wasn't very good at the game and wanted to get some encouragement.
The developers of the game were originally going to have Fox say "I guess it's your turn to be thankful" to make him sound cooler, but felt that the line was too showy for him. They instead gave the phrase to Falco, who says it after saving Fox from an enemy.
In the Japanese Versions of the game, after being shot down one of Fox's Teammates will shout out his name, similar to Star Fox Assault, but in the Western Versions, they instead shout "No!!!".
The game's opening features the phrase "Star Fox in Nintendo 64". This was a translation error and is supposed to read "Star Fox on Nintendo 64". This was fixed in the 3DS remake.
In the European version, there is an extra language called "Lylat", a made up language which is similar to the gibberish spoken in the original Star Fox.
In the Japanese version, the character icons do not sync with their voices and simply animate the whole way. This was changed in the western versions of the game where the icons would sync with what the characters are saying.
If the player takes too long to defeat the Golemech boss at the end of Venom's easy path (about seven minutes), the fight will end and the player will run into a wall, killing themself and making the fight restart.
In the Macbeth level of Star Fox 64, there is a time limit to fighting the boss even if the played missed the Supply Depot ending that leads to Area 6. If the player gets far enough, the boss will state that the player was too slow, and dive bomb the player, killing them instantly. If using a cheat to have infinite health, then the boss will continue to bounce the player upwards until the game crashes.
On the title screen, you can use the analog stick to move the "64" part of the logo around. Fox and his crew will watch it as it moves.
The planet of Katina is a clear reference to the movie "Independence Day". Similar to the movie, you have to dog fight aliens that are invading the world and if you do not finish off the mother ship in time, it will destroy the base with a blue laser. The new partner you get in this fight, Bill Grey, is a reference to the General William Grey from the movie.
The way the characters in the game talk by opening and closing their mouths was inspired by Thunderbirds and other "English puppet dramas" (called "Supermarionation" by Thunderbirds co-creator Gerry Anderson). Shigeru Miyamoto was a fan of these shows and imagined that if the Star Fox series became popular enough, AP Films themselves would come from England to talk about turning it into a "puppet drama".
After obtaining a gold medal on all levels, Expert mode will be unlocked. In Expert mode, Fox has his father's glasses.