Ho Yay: At the end of the second episode, Sonia kisses Sonic on the cheek for a job well done, and Sonic turns to Manic and says, "You're not gonna kiss me, are you?" Manic's answer? "No way, but you are kinda cute." One of the funniest lines on the show.
In another episode, Sonic asks for a dance while looking Sonia's direction. She accepts, but then he says he was talking to Manic, and the two begin slow dancing. The pair had a surprising amount of this.
Moral Event Horizon: While not quite up to the level of his Complete MonsterSatAM counterpart, Robotnik once tricked Manic with a robot made like a baby hedgehog in the hopes that he'd get attached to it...and reveal where Sanctuary, a place of refuge for children and infants was. So he could destroy it.
Another time, when confronted by a Chaos Emerald-fueled Dingo that was poised to destroy the planet, Robotnik was willing to let it happen if it meant the hedgehogs would die with it.
The Scrappy: Sleet and Dingo to some extent, as well as Bartleby.
Ship Mates: Rouge/Shadow fans that don't hate the guy, typically pair off Knuckles with Sonia (assuming they even acknowledge his other love interest, his distant cousin from the comics, Julie-Su).
Uncanny Valley: Some of the characters in this show really crawl close to this territory. (i.e. Just look at Sonia's adoptive mother in the first episode-she looks like something pulled out of a Renaissance Fair!)