These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crowning Moment of Heartwarming: Sharky and Eek hugging at the end of The Great Eekscape. Sharky is the one who actually initiates the hug. This was right around where the writers started giving Sharky more depth.
Hilarious in Hindsight: In "Eek Space 9," Scully realises Mulder was right all along when an alien spaceship crashes in her office; this was during the 1995-96 season, several years before Scully's conversion became canon on the live-action show! Made even funnier by David Duchovny and Gillian Anderson voicing their characters.
Just Here for Godzilla: The Terrible Thunderlizards segments. Yeah, who wants to see a bunch of obnoxious talking commando dinosaurs? Scooter and Bill the Cavemen are the real reason why we watch them!
Ugly Cute: Sharky again. Also Klutter, from his segments.