During one episode (titled BUG!, for those who are wondering) the animation for the episode was very Loony Tunes styled, which meant that the whole episode was a laugh-fest! Of course, there was one laughing spree moment where Manic landed on top of Sonic.
Episode 5 at one point had this gem:
Sleet: Why are we stopped for a puny tree!?!
Sleet (suddenly nonchalant): Ah. That's why.
Sonic goofing off by playing tennis with himself (AND serving as the referee) in "Last Resort".
From "The Price of Freedom":
Agent N: (introducing himself) Robotnik Intelligence Agent N, and you are hereby arrested for crimes against the state, and because... Dr. Robotnik HATESHEDGEHOGS!"
From episode 1.
Oracle: Come, Sonic! Your destiny awaits!
Sonic: Tell it to wait outside, I'm too tired to care.
The hedgehogs using the Do-Bot to erase Robotnik's memory of the cassette tape.
In "Wedding Bell Blues," there's this exchange.
Robotnik: Sleet, you idiot!
Sleet: No, sire. I'm the conniving one! Dingo's the idiot!
"Beginnings" has this exchange as Robotnik tries to figure out what the Resistance's secret weapon is.
Robot: Sensors indicate that the subject is blue, sir.
Robotnik:Blue? Is that all!?
"Getting to Know You" has this.
Dingo: (on Sonia) She's pretty.
Sleet: And you're ugly. Now let's get to work.
Sonic and Manic disguised as belly dancers in "Who Do You Think You Are?".