In issue 260 of Nintendo Power, Yuji Naka revealed that the initial concept for Sonic the Hedgehog's gameplay came from playing level 1-1 of Super Mario Bros. over and over again as fast as he could, since you always had to play the level first regardless of whether you used warp zones or not.
"I always tried to get through the level as fast as I could. And that inspired the initial concept for Sonic the Hedgehog."

Sonic was originally planned to have a human girlfriend called Madonna, whose design was directly based on the sexually provocative American pop singer of the same name. In line with this, character designer Naoto Ohshima designed Madonna to be attractive and to chase Sonic around (similar to how Amy Rose acts in later games), which he described as a "male fantasy". Aside from concept art, Madonna's only known appearance was in a 1990 tech demo for the TeraDrive, a Japan-exclusive IBM PC with a Sega Mega Drive integrated into it. There are two separate claims as to why Madonna was removed. Programmer Yuji Naka originally claimed in 1993 that Madonna's planned role was to be a damsel-in-distress, with Sonic needing to save her, and that she was ultimately dropped because the team wanted to move the series in a different, more orthodox direction to set it apart from Mario. However in 2009, Sega of America product manager Madeline Schroeder claimed to be the one who removed her as part of an overall effort to "soften" Sonic's image for younger audiences and foreign countries under the belief that Madonna was too Japan-esque. In 2015, Madonna would be reimagined by comic book writer Ian Flynn and appear in Archie Comics' Sonic the Hedgehog comic book series, having been redesigned to be an agent of G.U.N.'s C.L.I.P. division named "Madonna Garnet".

There's footage of a proto-type build of Sonic in the background of the Noah's Arcade ad in Wayne's World. The footage shows UFOs in Marble Zone. These UFOs were removed from the final build of the game.

In Act 1 of Green Hill Zone, it is possible to die by going too fast. At a certain point in the stage, the camera may not be able to keep up with you when you dip downhill, causing the game to think that Sonic has fallen into a bottomless pit.

Sonic was originally going to be called 'Mr. Needlemouse', a literal translation from the Japanese word for hedgehog.

According to series developer Yuji Naka, the iconic "SE-GA" jingle at the beginning of the game took up 1/8 of the game's cartridge space.

There are hidden embedded Japanese staff credits on the "Sonic Team Presents" screen. With the aid of a palette editor or cheat code, one can hide the title card and invert the colour of the background to make it visible.

In early screenshots of the Genesis game, a UFO could be spotted, but was not present in the final game. Yet when Sonic the Hedgehog was released in 2005 for mobile phones, the UFO sprite was found hidden away in the files, but still unused.

The game's soundtrack was composed on an Atari computer.

The Japanese band "Dreams Come True" are credited with composing the game's entire soundtrack. To promote their first tour, the band had concert posters with Sonic the Hedgehog on them, and painted Sonic on the side of their tour bus.

Scrap Brain Zone was originally known as 'Clock Ork Zone'. It's believed the name was changed because it was planned to be called 'Clock Work Zone', but no 'W' existed in the game's zone title font.

In the game's code there exists a sprite of a Goggle monitor, and some matching goggles to go with it. There is also an unused sprite of Sonic holding his breath, meaning these were likely once an underwater power up.

Within the game's data is a set of unused sprites showing Sonic shrinking or falling away from the screen.

The Japanese version of the game has more parallax scrolling layers. An example would be that the clouds in some of the zones move across the screen, while the international version the clouds are stationary. The Labyrinth zone also has an underwater wave effect in the Japanese version. The only zones that were not changed were the Starlight zone and the Final zone.

In the original international release, a short cut taken to the finish in the Labyrinth Zone would only allow the player to collect a total of 49 rings, missing 1 ring from going to the special stage. However, in the Japanese version, a ring was added so that people could get to the special stage if they went this way.

In an early version of Sonic The Hedgehog shown in a pilot episode for the TV game-show "Nick Arcade", a rolling ball can be found towards the start of Green Hill Zone Act 1. This was removed from the game's final release.

Hirokazu Yasuhara was going to go to America to establish a new development team but because of the Gulf war between Iran and Kuwait, his trip was delayed. Yuji Naka and Naoto Oshima noticed him being upset and decided to let him join their team temporarily until he leaves. He ended up staying for a year to design the levels for major games such as Sonic the Hedgehog.

It's possible to play the game using an Atari 2600 controller, as every button besides start works as a jump button, and thus the game is fully playable despite the controller only having a single button.

The title screens of Sonic the Hedgehog and Sonic the Hedgehog 2, with Sonic (a character known for his super speed) posing and waving his gloved hand inside of a ring lined with stars and a ribbon banner at the bottom, could possibly be taken from the logo of the 1981 anime adaptation of the Akira Toriyama manga "Dr. Slump" and its speedy protagonist Arale. It should also be noted that the ring surrounding Sonic has giant wings protruding from its sides, which appear to reference the angel wings on Arale's cap that also feature in the intros to the anime and some of the Dr. Slump films.

While it's not known if any Sega employees have commented on this connection, it was acknowledged in the form of a small cameo appearance where Sonic gets outrun by Arale in the 1993 sequel manga "The Brief Return of Dr. Slump".

The appearance of Longclaw in Paramount’s Sonic the Hedgehog films is reminiscent of the tiles that resemble an owl's head in the Labyrinth Zone from the original Sonic the Hedgehog. In fact, the first film's opening scene features the tile design engraved on a rock as an Easter egg, further hinting at the connection.