The episode where Sonic is trapped in a world where Eggman is the leader of it, if only for that B-Plot with Eggman and his shapeshifting brother from another dimension trying to convince everyone that his shapeshifting brother is actually Sonic even when he fails horribly.
I also enjoyed Eggheads and that climax with Sonic feeding Eggman his own modified cookies to turn him into another Sonic.
Mayor Knuckles as well for being funny throughout.
Two Good To Be True for giving us the ultimate hammy Knuckles.
Fiendbot was much sweeter than it really should have been being just another Iron Giant rip-off...
Fuck it, this show was glorious through and through...