Being a big fan of Karai, I'll always consider episodes like "New girl in town", "City at war" and "Broken foot" among my favorites. The banter between her and Leo is just so funny, they act like they have been married for 20 years.
But there was more humor in those eps.
From "New girl" after taking over leadership of the Turtles, Raphael displays a more hands on approach than Leo.
Donnie: I'm working as fast as I can Raph.
Raph: Then work FASTER!
Donnie: Do you think yelling is going to help?
Raph: No I think HITTING is going to help.
Donnie: I'll work faster...
Raph takes the others on their first mission with him leading, the search for Snakeweed leads them into a far dirtier part of the NYC sewers.
Mikey: Man it really stinks in here!
Raph: It is a sewer Mikey!
Mikey: I mean more than usual, where does all of this stuff come from anyway?
Raph and Donnie exchange a look.
Donnie: Actually Mikey most of it comes from... (He whispers something into Mikey's ear.)
Mikey: WHAT?! DON'T PEOPLE KNOW WE'RE LIVING DOWN HERE?
After not getting any info about the mission from Raph, Leo sits watching TV, watching "Space heroes" where Captain Ryan is seen passionately making out with a blue skinned woman.
Celestia: We shouldn't be together Ryan, it is against your fleet's protocol.
Ryan: Well Celestia, you don't get to be captain of the Dauntless by following all the rules.
She whips out a gun.
Celestia: Good then you wouldn't mind giving me the codes!
Ryan: Celestia.. You've broken my heart!
He pushes a button and vaporises her.
Ryan: But my disintegrater ray still works!
With a sad look he picks up her boots.
Ryan: At least I have these to remember her by.
Leo: Boy relationships are complicated!
Here's a piece of trivia: Ryan mentions the name of the ship being "The Dauntless." Which means it's named after THIS.
The Douglas SBD Dauntless was a carrier operated Dive bomber which most famously flew off THIS carrier.
The USS Enterprise, which makes the circle round again concerning the Star Trek references.