Spoiler:In the ending cutscene Chip says "sonic you must live", but the subtitles mistakenly say "sonic you have to live"
Knuckles and Shadow were planned to be in the game but the idea was scrapped for unknown reasons.
The lead composer of the game, Tomoya Ohtani, uses musical samples in some of his tracks for the game, similar to how Hideki Naganuma and Ohtani himself used samples in Sonic Rush and Sonic Rush Adventure, respectively. One amusing coincidence is that the intro of Windmill Isle is based directly from a remix of a track from the arcade-only game Ollie King, which Naganuma composed the entirety of.
In the original concept work of the character "Chip", his name was "Whip", referring to whipped cream, as whipped cream was an early design motif. However, this was changed as some felt the name whip carried too many negative connotations in English (such as whipping as an act of punishment, or the injury known as whiplash).
In the Daytime Spagonia stage (Rooftop Run) on both the PS3 and Xbox 360 versions of Sonic Unleashed, in the middle of one of the curves, a pedestrian will be reading a newspaper. Upon further inspection, there is a, albeit blurred, picture of the box art for Sonic the Hedgehog (2006) to the upper right of the paper.
Many of the Street Locations are named after other Sonic characters that don't appear in the game; more specifically the members of Team Dark (Shadow, Rouge and E-123 Omega), Silver, Blaze, Pachacamac, and the Chao. Exceptions to this include Knuckles and Cream.
In the Werehog side missions, there is a place called 'Soleana Hotel'. This is likely a reference to Sonic The Hedgehog (2006), which was set in the similarly spelled 'Soleanna'.
The term "Werehog" is derived from the words werewolf and hedgehog. However, this is a misnomer, considering that the "were" in werewolf derives from the Old English "wer", meaning "man", which means he is incorrectly referred to as a "Manhog". A "Manhog" would be a man who can morph into a pig, or someone who is half man, half pig.
In Eggmanland, there are three robots whose names represent a console and a year that a Sonic game came out. These are EF-MD1991 (Mega Drive/Genesis and Sonic The Hedgehog), EF-DC1998 (Dreamcast and Sonic Adventure), and EF-XB2006 (XBox and Sonic The Hedgehog 2006). To further cement this idea, MD1991 was made first while XB2006 is the youngest and is apparently clumsy, glitchy, and can't do anything right.
During the opening cutscene, just as Eggman is about to fire the laser, you can see a Sega Dreamcast behind him.
Near the end of the game, Spoiler:after the Egg Dragoon is defeated, Dark Gaia will emerge. When it goes back to Eggman (before he is hit by Dark Gaia), to the left of Eggman (his right) is a SEGA Dreamcast.