According to the "ALL ABOUT Capcom Fighting Games 1987-2000" book, Alex was originally supposed to be the main character of SF3, but this was changed because he wasn't recognized as a hero character compared to Ryu.
Chun-Li makes a cameo in Ryu's background during the New Generation and 2nd Impact games; she can be seen bathing on the top left of the stage.
One of Chun-Li's win quotes in the game is "Hey leave me alone. I'm a fighter, not a news reporter." This may refer to the Street Fighter live-action movie, where Chun-Li was portrayed as a news reporter.
Screens from early versions of the game show that Ryu originally had different art at the select screen. This early version also has different colors on the HUD, and the "PLAYER SELECT" text was blue instead of yellow.
Checking in the sound test reveals that all of the Super Art moves for each character have the garbling effect (used when the character Twelve transforms via X.C.O.P.Y) recorded for them, even though the use of the Super Gauge as a timer means that Twelve cannot use any of his opponent's Super Arts in-game. This possibly indicates that Twelve was going to be able to use Super Arts from his opponents at one point.
In the game's data there is a unused remix of the "Jingle Bells" Christmas song. Considering Sean's stage is a Christmas-themed New York City, it's possible that this was his original theme.
A prototype version of Hugo can be found in the game data for Street Fighter III: New Generation, with only his basic moves finished and placeholder graphics. Performing certain attacks on him may cause him to become invisible or freeze the game.
In the Japanese version of Street Fighter III: 3rd Strike and 2nd Impact: Giant Attack, when Urien loses to his opponent by time out, he squeezes his arm, which spurts out blood. The blood was removed in the International version.
When a character obtains a full bar of their super meter in 3rd Strike, the phrase "Let's Go!" can be heard. This is actually a sample from the 1960s Batman TV show; specifically the line "To the Batmobile! Let's Go!"
In the Japanese version of Street Fighter III: 2nd Impact, "Akuma's" blood is red in his defeated portrait, but in the International version, they colored it in green.
In Street Fighter III: New Generation, when loading the main menu the game also loads in an unused image for a ghost that looks very similar to the Ghosts from Pac-Man.