The Super Emeralds are shaped in a brilliant diamond cut. The color of the Super Emeralds match the colors used in Sonic 3. The only difference between this and current canon colors is that an orange Emerald is used in place of yellow. The Super Emeralds are also much larger than the Chaos Emeralds.
Sonic the Hedgehog 3 & Knuckles
In Sonic the Hedgehog 3 & Knuckles, when a player enters a flashing Giant Ring for the first time, they are transported to the Hidden Palace Zone, where a number of giant, dull gray Emeralds will appear depending on the number of Chaos Emeralds that the players have collected to this point. When the player steps on these dull Emeralds, they are transported to a new Special Stage (identical to those that appeared in Sonic & Knuckles), where they have a chance of winning a Super Emerald. If they succeed, the Emerald in the Hidden Palace that they originally stepped on will light up to their original colors. Jumping through another flashing giant ring will again transport the player to the Hidden Palace for a chance to win another Super Emerald, until all seven Super Emeralds have been collected. (Note that traveling to Hidden Palace for the first time disables the player's ability to activate a super transformation, if all Chaos Emeralds had already been collected.)
Getting all the Super Emeralds makes the Master Emerald glow, and enables Sonic to transform into Hyper Sonic, Tails to transform into Super Tails, and Knuckles to transform into Hyper Knuckles. These "Hyper" forms are improvements over the usual "Super" forms, with increased speed and power, along with powerful new abilities.
In the Sonic the Hedgehog comic series and its spin-offs published by Archie Comics, the Super Emeralds, also referred to as Super Chaos Emeralds, appear as their own independent objects rather than transformed Chaos Emeralds. However, their appearances and history are very inconsistent.
In this media, the Super Emeralds were seven special Chao who turned into Emeralds from stopping Perfect Chaos' first rampage. After freeing Chaos, Dr. Eggman sought the Super Emeralds to make Chaos invincible, but was foiled. Chaos eventually managed to get the Super Emeralds itself and become Perfect Chaos with them, but it was defeated and the Super Emeralds reverted back to Chaos again.
The Super Emeralds are the first instance of Emeralds in the Sonic the Hedgehog series having brilliant diamond cut (the Master Emerald, which also has a brilliant diamond cut, was also introduced in Sonic & Knuckles).
In Mushroom Hill Zone, it is possible to collect all seven Super Emeralds- three in Act 1 and four in Act 2.
Strangely, when the red Emerald is obtained and then either the blue or yellow Emerald, the red Emerald appears dark violet.
The Super Emeralds can be very easily gained by activating the Level Select code and repeatedly winning "Special Stage 2". The Emerald itself would be yellow but the game would think the player gained the other ones and the player will still be able to get the Hyper forms after it says the character got all the Super Emeralds, despite gaining the same yellow Emerald. They won't appear in the Hidden Palace with the Master Emerald though, but the player will still get the best ending.
In Sonic Adventure, when the player sees the past version of the Altar, the Chaos Emeralds shown there are, in comparison to the Master Emerald, about the same size as the Super Emeralds. They are also larger than the Chaos Emeralds in the rest of the game, and referred to simply as "the Emeralds". It is highly likely that these are the Super Emeralds, though they are never referred to as such.
Takashi Iizuka has stated that the Super Emeralds were added to Sonic the Hedgehog 3 & Knuckles after the game was split in half, serving as lock-on bonuses to enrich the experience for players who had already collected the Chaos Emeralds. He also indicated that the Super Emeralds (and other similar collectibles) will not return to the series anytime soon, as the number of Emeralds was made consistent as of Sonic Adventure.
Despite what Iizuka said, the Super Emeralds returned in Sonic Mania.
↑At Sonic Boom 2013, Takashi Iizuka said (as translated by the Q&A board's translator) "So Sonic 3 and Sonic & Knuckles had...the lock-on, and...for people who played Sonic 3 the first time, they went through and they collected all the emeralds, right? ...So you already played Sonic 3 and you go to play Sonic & Knuckles, you've gotta have more emeralds to collect...and we put the Super Emeralds right there... Going forward, y'know, we also have...the Super Emeralds, the Master Emerald, and there's all these emeralds, and we've got too many, so when we released Sonic Adventure, we went back and just sort of cleaned up all the Emeralds and kind of reduced that down so we can have a little more control." http://www.youtube.com/watch?v=0nzxRoIX4QU at 19:40