This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Sonic Underground
In episode 3, there's a quick shot of Trevor the mouse being interrogated. He has invasive wires◊ going into him.
Some of the background Mobians fall deep into the Uncanny Valley.
In "The Price of Freedom," Robotnik invents watches that watch people.
The Do-Bot brainwashing people to spill their real feelings about Robotnik. Even creepier is that she isn't aware of what she's doing.
In one episode, a Chaos Emerald-fueled Dingo was poised to destroy Mobius. Robotnik was willing to let it happen, saying that he didn't care what happened to the world so long as the hedgehogs went with it.