Super Emeralds

The Super Emeralds (スーパーエメラルド Sūpāemerarudo?) are a set of seven emeralds that are transformed from the Chaos Emeralds with the help of the Master Emerald, and are basically an enhanced version of the Chaos Emeralds. These Emeralds made their first and only appearance in Sonic the Hedgehog 3 & Knuckles, in which, they were the collectible items (replacing the Chaos Emeralds) in the second half of the game (the Sonic & Knuckles levels).

Description
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.

Collecting
In Sonic 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 date. When the player steps on these dull Emeralds, they are transported to a new Special Stage (identical to those that appeared in the unconnected 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.

Trivia

 * 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.