1. Espio's render during the opening sequence and his victory pose render in-game are referencing his sprite on the title screen in Knuckles' Chaotix. There are a few differences however, mainly the facts that Espio faces the other way and that he's frowning instead of smiling.

2. On the character select screen, Espio's CSS icon sprite references his old Knuckles' Chaotix sprite.

3. Speaking of the character select, Knuckles' CSS icon sprite references the cover on the Knuckles the Echidna Archives Volume 4 comic made by Archie. However, Knuckles in his CSS icon sprite is smiling instead of frowning.

4. The South Island stage references Green Hill Zone from the first Sonic the Hedgehog game.

5. The Casino Night stage references none other than Casino Night Zone from Sonic the Hedgehog 2.

6. Aurora Icefield bears a strong resemblance to Ice Cap Zone from Sonic the Hedgehog 3 & Knuckles, except for the fact that Aurora Icefield takes place at night.

7. The Mushroom Hill stage references Mushroom Hill Zone from Sonic 3 & Knuckles.

8. The Death Egg's Hangar stage bears a striking resemblance to the Silver Sonic battle arena from Sonic the Hedgehog 2.

9. Fang's fighting pose is similar to that of Ryu, Ken, and Akuma's in the Street Fighter 3 series, even though this game came out before Street Fighter 3.

10. Sonic and Knuckles share the same idle fighting stance.

11. Espio's jump attack in this game is similar to that of his spin dash and jump attack in Knuckles' Chaotix.

Some Others I would like to add:

In the game data, there is a character for Eggman out of his mech, with his own moveset. He even has his own losing animation!

While you can hack to play as Rocket Metal and Eggman in his UFO thing, they do not have unique movesets and instead default to Knuckles' moveset.

If you hack to play as them, Metal Sonic and Eggman (without the mech) actually have their names rendered in the end ranking screen, which possibly indicates that they were intended to be played, but were scrapped at some point.