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In a 1999 interview with the game's director and designer Masahiro Sakurai published in Nice Games magazine vol.3, he was asked if he ran into trouble with getting permission to use Nintendo characters? He responded:

"The first person I asked for permission was Shigesato Itoi. Next was Shigeru Miyamoto. When he saw our work he said, “Hey, you’ve got Mario down pretty good!” The Pokemon characters took the longest to get permission, because their image is tightly supervised. I broached the subject with Pokemon Company president Tsunekazu Ishihara, but the impression I got from him was that it would probably be difficult. Satoshi Tajiri was more encouraging—he was like, “this looks cool!”"

"Personally, as the creator of Kirby, I understood how they felt: I would feel be really upset if Kirby was featured in a game that people ended up disliking, or if the people got his image and movements wrong. In fact, there had been times when I’d been kind of annoyed by the way Kirby was depicted in someone else’s illustration or as a game cameo. Smash Bros. was conceived, in part, as a reaction against that kind of sloppy handling. I imagine anyone who creates a character feels similarly protective, but Smash Bros. brought an unprecedented number of different characters together and it was of the utmost importance to us that we re-create their personalities and characteristics faithfully. I absolutely did not want to betray the original characters’ creators."
Contributed by ProtoSnake
Mario and his Special Moves in this game are based off of the "Shoto" style of Fighting Game characters, most specifically the character Ryu from Street Fighter. For example, like Ryu, Mario has a Hadoken-like "fireball" attack with his Neutral Special (Fireball), A punching uppercut similar to the Shoryuken via his Up Special (Super Jump Punch), and a spinning tackle akin to Ryu's Tatsumaki Senpukyaku in the form of his Down Special (Mario Tornado). However, while Mario's moveset would change in later games to be less Shoto-esque, Ryu himself would be added into the Smash series and make his debut as a fighter in Super Smash Bros. for Nintendo 3DS and Wii U.
Contributed by PirateGoofy
The 3D portraits on the character select screen are based on character artwork from some of their home games. Mario's render is from Super Mario 64; Link's is from his artwork for The Legend of Zelda: Ocarina of Time; Donkey Kong's Donkey Kong Country artwork is the basis for his Smash portrait; Yoshi's comes from Japanese artwork for Yoshi's Island; Kirby's is from Kirby's Adventure artwork; Fox's is taken from Star Fox 64; Captain Falcon has a 3D realization of artwork from F-Zero X; Pikachu and Jigglypuff are 3D versions of Pokemon Red & Blue concept art; Samus Aran's comes from Super Metroid; Ness's is a redone done version of his EarthBound art; And Luigi's appears to be taken from Mario Kart 64.
Contributed by PirateGoofy
Marth was originally going to be part of the roster, but was scrapped due to time constraints. He later made his appearance in Super Smash Bros. Melee as an unlockable character.
Contributed by MeleeWaluigi
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According to his character bio, Kirby is only 8-inches tall.
Contributed by Boyobmas
On Hyrule Castle, the Maxim Tomato item never appears, making the Heart Containers from The Legend of Zelda universe the only major healing item to appear. If it is the only item put on using the item switch, all boxes and capsules will either explode or be empty.
Contributed by Rainbow Pancake
The game's official US website refers to the Bob-omb item as "Bomb Soldier".
Contributed by Boyobmas
The bedroom seen in the intro and in the scene shown after completing 1P Game has a door that is always completely unseen. Since the camera focuses mostly on the table where Master Hand puts the dolls on, the door stays hidden behind the camera.
Contributed by xianc78
Captain Falcon and Samus share multiple attack animations.
Contributed by CosmykTheDolfyn
In the Japanese release, the attack sounds are real punching noises. It's likely this was changed to keep the game family-friendly.
Contributed by GamerBen145
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In the Mushroom Kingdom stage, pausing the game and looking off to the left or right of the stage to see outside of the standard gameplay field of view, it's possible to see walls with warnings signs reading "Danger" on them, warning the player of the stage's boundary. This appears in the stage in Super Smash Bros. Melee too.
Contributed by GamerBen144
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The banner in the background of Saffron City that says "Got a Catch 'em All!" in the Japanese version, missing the second T. This was changed to "Gotta catch 'em all!" in the Western releases. The font also appears to have been rewritten to accommodate this. Also, the Silph sign on the Building on the right is Romanised as Silf in the Japanese release.
Contributed by CuriousUserX90
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In an early version of the game, Saffron City's rooftop had a pink and purple color scheme.
Contributed by GamerBen144
There is an unused sound of the announcer saying "draw game", suggesting this may be an early name for Sudden Death, or possibly that sudden death originally didn't exist.
Contributed by xianc78
In the Japanese version, there is an unused voice clip of the announcer saying "Jigglypuff!", however Jigglypuff's Japanese name is Purin. This seems to hint that the developers planned to release the game in the west from the start, as Jigglypuff is the only character whose name is different in English and Japanese. This voice clip is also different than the one used in the international release of the game.
Contributed by Takahashi2212
The congratulation screens were absent in the Japanese version of the game.
Contributed by xianc78
After the Super Smash Bros. release in Japan, Nintendo began a poll to gauge public interests for future roster additions. Of the top ten, seven have since been added, with the remaining three left out. James Bond was most likely left out due to legal reasons, as he is not originally a video game character and belongs to a more strict estate. While not playable, Mew and Toad both make cameos with Mew being a rare Pokeball result and Toad being used in one of Peach's attacks in later games.
Contributed by LamerGamer
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One of Peach's Castle's hazards is a bumper, which is mostly used as an item. Coincidently, this is the first stage to use an item as a hazard, and have a hazard outside of its own universe; Peach's Castle is from Mario and the Bumper is from Super Smash Bros.
Contributed by JelloBoyInc
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In an early version of the game, Peach's Castle lacked the sign, the bridge, and the sliding stone blocks.
Contributed by GamerBen144
In the background of the Mushroom Kingdom stage, Green Koopa Troopas can be seen walking back and forth across platforms. This contradicts every Mario game to date where Red Koopas turn when coming to an edge while Green Koopas will simply walk off the edge.
Contributed by Boyobmas
Captain Falcon and Ness are the only playable characters who do not have a stage based on their respective franchises.
Contributed by CosmykTheDolfyn
Super Smash Bros. was developed with a low budget, had low publicity when it launched in Japan, and was even intended to be Japan-exclusive. However, the game's success prompted Nintendo to localize it for international audiences.
Contributed by game4brains
For some reason, the announcer says Fox differently in the Japanese version than in the International version, even though Fox is a character with no name differences in any region.
Contributed by Takahashi2212
The Fighting Polygon Team is called Dummy Corps in the Japanese version.
Contributed by ClaudX
According to a page on the Japanese Super Smash Bros. site, Mewtwo was planned to be playable, but was cut; Bowser and King Dedede are also mentioned as having been cut, though no other information is available.
Contributed by ClaudX
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Charles Martinet is misspelled as Charles Martinee in the game's credits.
Contributed by DeerBoarDude
It is impossible (at least without the use of a cheat device) to clear all eight digits in the points counter in 1P mode.
Contributed by xianc78
Captain Falcon has the most usable costumes in the game, with six. Most characters have four or five. Yoshi also has six, but only four are usable outside of hacking, as two only appear in the single player mode.
Contributed by Boyobmas
When the Announcer introduces Metal Mario, his voice becomes slightly metallic. Although it may just be to place emphasis on Metal Mario's metal composition, the Announcer's voice sounds noticeably deeper and it does not change like that for any other character in Classic Mode.
Contributed by ClaudX
Luigi takes his appearance from Super Mario World, having purple overalls rather than dark blue. However, this is not true of his artwork.
Contributed by ClaudX
Captain Falcon's "Congratulations!" screen is the only one to use a pre-existing image from an original game, in this case, the first unlockable title screen from F-Zero X.
Contributed by ClaudX
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Captain Falcon is the only playable character that doesn't use his own head for his stock life icon. Instead, he uses a Falcon.
Contributed by ClaudX
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While all other characters show their skeletons upon being hit with an electric attack, Samus's suitless outline becomes visible instead.
Contributed by ClaudX
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In the character select screen, the characters (excluding unlockable characters) are placed in the order of when they first appeared in their respective titles, starting with the oldest, Mario and Donkey Kong, and leading to the most recent, Pikachu.
Contributed by ClaudX
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According to an interview with Satoru Iwata, Masahiro Sakurai intended for the characters to use Final Smashes in this game. It was taken out due to hardware limitations. This concept was held off until Super Smash Bros. Brawl. Going in the debug menu you can find 3 sound files. 2 of them of Ness saying "PK" and "Starstorm!". The third is Captain Falcon saying "Come On!".
Contributed by Bean101
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The original prototype for Super Smash Bros. was a four-player fighting game designed by Masahiro Sakurai and programmed by Satoru Iwata tentatively called "Dragon King: The Fighting Game". The game was designed specifically for the Nintendo 64's joystick to see how it could be used in a multiplayer environment. The signature concept of Nintendo characters fighting each other was not initially present, but would soon be implemented as the first idea Sakurai thought of to make his game stand out, as fighting games did not sell well and most of his original concepts felt better suited for arcade fighting games rather than home-console fighting games. A subsequent prototype featuring Mario, Donkey Kong, Samus, and Fox as playable characters was then made without sanction from Nintendo's higher-ups and they were not informed of its existence until Sakurai was sure the game was well-balanced. When Iwata initially presented the idea of the game to Shigeru Miyamoto to gain approval for the use of Nintendo characters, he turned it down. However, Iwata did not tell Sakurai this and convinced him to pitch the prototype to Miyamoto anyway, which later got his approval.

Little is known about Dragon King's gameplay or design, and all information known about the game comes from interviews and a handful of images shown when the game was in an alpha stage. No gameplay footage has been demonstrated, and a working prototype has not been made publicly available. Images of the game, however, show that much of the core gameplay was similar to Super Smash Bros., featuring damage percents, arenas with platforms, and combatants that do not strictly have to face one another. The tall, thin build of the unnamed fighters and their kicking and punching techniques also appear to be relatively similar to that of Captain Falcon. The most widely-known stage background featured in the screenshots is a photo taken by Sakurai of a Ryūō-chō neighborhood in Yamanashi, Japan, which is where HAL Laboratory's headquarters are based, where the game was being developed, and what the prototype was named after. The "Ryūō" in Ryūō-chō means "Dragon King".
Contributed by kirbologist