These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Angst? What Angst?: Mario seems to be more upset that Luigi died in Season 2, as it was a motive for him gathering his friends to kill Sonic, but in Season 6, he doesn't seem fazed when Soniqua spits fire at Luigi.
Lucca doesn't seem upset when her Epoch is destroyed in the near-ending of Season 6, and lets Tails and his friends to borrow the other time machines with no problem.
Awesome Music: The 16-bit rendition of Song 2 by blur that plays during Sonic and Tails' fight.
Gangnam Style's 16-bit rendition. Played in one episode where Tails keeps on listening to it and played in another episode when Sonic and the gang minus Tails have a party with Eggman-mutated Zerg...
It also plays VERY briefly in the timeline where Gilius Thunderhead takes Sonic's identity.
Don't forget about the rendition of "Here I Go Again" by Whitesnake. Sure, it only plays for 10 seconds (thus making it a Long Song, Short Scene situation) but if you listen to it in full on Mike Monk's soundcloud then you'll know what I'm talking about.
And Push It To The Limit.
And their rendition of Joe Esposito's "You're the Best" during "This Can't Be Good".
Crosses the Line Twice: Tails has been bullying Sonic a bit in Season 4, but he sends in a freaking bomb just for no reason at all.
Sonic killed Crash Bandicoot in a way similar to Taken, and then asks him if he did a good job imitating it, WHILE Crash was still being tortured.
The Starcraft episode focuses on Zerg assimilating DNA, which is something that is known in the backstory. Come Starcraft II Heart Of The Swarm, where you get to see this DNA assimilation in action ... although the Zerg have to kill to assimilate the DNA ... Eggman didn't die.
The episode before the season 6 finale had someone comment that Jim in the form of Yoshi would eat baby Eggman and only to hatch him out again.
Duck Hunt Dog was shown to be aggressive in an episode of Sonic for Hire. Come to the fourth Super Smash Bros. game, the Duck Hunt dog is revealed as a character. Many people wondered if the Duck Hunt Dog could be seen as a fighter instead of a punching bag.
It's Short, so It Sucks : Some people think the episodes are way too short. Lampshaded by Sonic in one particular episode.
Sonic: Ok, I know this episode was short but I might die next week! Doesn't that mean anything to you guys?! Jerks!
Jerkass Woobie: You've got to feel bad for Sonic in Season 4... after Tails screwed him over. Let's see... he was trying to be nice to him at Burger Time, but Tails threw a shake at Sonic.
He also ran over Elliot when Sonic was helping him build E.T's phone leading to Sonic getting arrested.
Its also said in the first episode that Tails knew Sonic would lose all his money in Dreamcast and gave him the stock tip in the first place.
Tails: Lets not get into all the details about who purposely screwed who out of all their money.
Take That, Scrappy!: The opening of Season 5 is basically a huge one for Tails. Sonic punches him several times, neither Peppy nor Slippy have heard of Cash Explosion, and when he assumes that he'll be taking charge of the Star Fox Peppy outright says no and picks Sonic instead.
The next episode ups it further by making Tails being attacked by a number of Facehuggers, ending with a Chestburster coming out of him. And later on in the Starcraft episode where they all leave him holding up a wall while Eggman-mutated Zerg and the gang have a party.