My favorite episodes are Episode 36: "Mission to the Sun"; Episode 28: "Robot Randy"; Episode ??: "Hunchback of Nowhere". In Mission to the sun, all three characters are sent to the sun to keep it from fizzling out (just a cartoon), and along the way, a micro-sized alien worm by the name of "Mustafa L. Bacterius" gets inside the brain of Muriel to control her and make her wreck the ship.
Quote: "My name is Mustafa Al Bacterius. I am inside the brain of Muriel. I have come a great distance to sabotage your mission. You humans are not satisfied messing with your own planet. You feel the need to mess with space also. Well, if the sun wants to fizzle, let it. We like it dark. So get a flashlight and some D-Cells, cuz it's lights out!!"
In Robot Randy, a giant robot (bigger than a house) from an alien planet is sent to Earth by his superior to conquer it. Basically, he doesn't want to destroy things, so he intentionally misses targets on his planets when the robots gather together to show their destructive skill. They laugh at him and call him a failure, and upon landing on Earth next to Courage's home, he enslaves the three main characters, making them do all kinds of grueling work (a la, ancient Egypt). However, in his private time, he likes to carve reindeer out of wood. This one was rather touching.
Funny Fact: the robot's voice is based on Christopher Walken's (actor)
In the episode with the hunchback, an ugly but very kind old man goes house to house looking for a place to spend the night during the thunderstorm. All people reject him immediately, even Eustace, one of Courage's owners. Later, Courage is sent to the barn to fetch Eustace's raincoat, and Eustace scares Courage with a pair of fake pop-out eyes (Courage gets scared at almost everything). He gets to the barn to hear bells being rung, and finds the hunchback in one of the second floor open hay lofts. Courage comes over and sits down next to him, and watches him ring bells sadly. Then, courage rings one, and the man lights up, and they both ring some bells. The next scene shows them interacting playfully in activities to some groovy touching music. You know what, just watch the episode yourself (those who haven't seen it). My hands are getting tired.