Seeing the Decepticons get drunk on Energon in "Micro-Bots" is probably one of the funniest moments in Transformers history. Megatron slurs his words and rambles about Cybertron being "The Home of the Metal Moon" and Laserbeak flies like he's drunk and crashes.
Megatron (to Starscream): "You're either lying, or you're stupid!"
In "Enter the Nightbird", there's a scene where all of the first season Autobots chase Nightbird up a cliff. The one Autobot that needs help getting up the cliff? Cliffjumper.
In "Megatron's Master Plan", there's a scene with Soundwave and all his tapes at a dance club. Rumble's dancing, Soundwave's chillin' with the ladies and some random guy asks Laserbeak if he wants a cracker. Laserbeak's eyes glow in response. This reaction could be interpreted as anything from "I will destroy you, human" to "Mmm, crackers..."
Ultra Magnus (entering the core chamber of a planet to nuke it): "I've never seen anything this beautiful in the entire galaxy. All right, give me the bomb."
In the pilot, when Ironhide diverts a flood, a human says "Thanks, neighbor!"
In "Quest for Survival", Megatron, Starscream and Soundwave encounter some sort of metallic plant life. Megatron warn Starcream from attacking it, but Starcream shoots the plant anyway. His laser bounces off the plant and hits him straight back. Megatron and even Soundwave laughs.
While the concept of the madness plague in "The Return of Optimus Prime" is pure Nightmare Fuel, Evil!Ultra Magnus after he's infected is so overthetop that it's hard not to laugh, to the point that he starts making the Decepticons look subtle. Especially his epic delivery of "YOU CAN'T ESCAPE, RODIMUS! I CAN TRACK YOUR GAS FUMES ANYWHERE!"