Metal Sonic from Sonic CD can be seen in the background of Eggman's lab.
If you play Tails campaign from beginning to end without stopping, his eyes will be half closed because he is so tired.
In Mission mode with Sonic, on one mission, you have to collect 100 rings and go to the Sonic billboard. The Sonic Billboard is the Sonic X logo with Sonic and Chris on it!
You may recognize the music in the third part of Windy Valley : it is in fact the music of the level Green Grove in Sonic 3D.
At some points of the "adventure" (for example, when you finish Casinopolis with Tails), you may notice a rabbit flying around. It is Cream, a character from "Sonic Advance 2" and the "Sonic X" TV show.