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.
Anvilicious: All episodes end with a short snippet where a presenter summarizes the lesson of the week and dishes out the appropriate Bible verses.
Author's Saving Throw: The writers goofed and gave Lucy's last name as Cunningham in one episode and Schultz in another. The explanation became that her father died and Shultz was her stepfather's last name, and from then on she was Lucy Cunningham-Schultz.
Fridge Brilliance: Campbell County Community College accepted Eugene when he was VERY YOUNG, and considering he was (as far as the state knew, anyhow) an orphan, they also took care of him. He stayed with them out of gratitude.
Genius Bonus: In the episode "Stage Fright"; a School Play where the Jones and Parker Detective Agency are investigating a mysterious noise is held at the Taft-Hartley Theater. In universe the theater is named after two local actors; but it also serves as a reference to the 1947 Taft-Hartley Act; a bill passed in response to a series of 1946 strikes that outlawed the "closed shop"; sought to prevent Communists from gaining leadership in unions and allowed states to institute "right-to-work" laws that would prevent unions from excluding non-union workers.
Idiot Plot: The episode "Buried Sin". It's mildly understandable that a kid would think he'd committed murder when a gun he was holding went off and killed someone, and that the descendant of said victim who is currently a child may think that, but Whit? Pretty much everyone else? No... That's not murder. No court in the US would charge him with murder for accidentally killing someone. I mean, considering his age, he probably wouldn't even get a manslaughter charge. His father would have been charged with negligence for leaving the gun where his son could get to it, and for not teaching his son proper gun safety. The child would not have been held responsible.
Irony: An early episode about facing your fears ended terrifying several children who had never had such a problem before.
The episode where Eugene experiences what Hell would be like for him.
Dr Blackgaard has a few of these, but his resurrection is particularly horrific. Abraham Lincoln going on a killing spree? And he was about to kill a little girl before Whit intervened.
The Marquis of Matrimony from "The Marriage Feast" (an adaption of the story in the Book of Matthew). Unlike the Duke of Terra and the Countess of Bovine, he is against the emissaries right from the start, and then orders them to be tortured; which leads to the actual death of one of the said emissaries.
Tear Jerker The biggest, for me, is in the Novacom arc, when Whit is taking Connie home from their FBI encounter after he told her that Mitch died, and she says she's OK. Whit lets her out, and she comes back to the car a few moments later, opens the door and says "I'm not OK, Whit! I'm not OK." Even though I know how it turns out, that scene never fails to get the waterworks going.
"Mortal Coil", "Gone", "Underground Railroad", "Where is thy sting", "Karen", "Forever, Amen"... There are quite a few tearjerker episodes.
Meta example for "Mortal Coil". It originally aired very close to the Thanksgiving holiday so many families only heard the first part, leading to many hysterical children who were very worried that Whit had died.
Life Expectancy, in the most recent album. Connie's mom dies of a heart attack, it kills her instantly.
What Do You Mean, It's for Kids?: The show's audience is undeniably children, but there are episodes that sort of blur the line and don't seem to be appropriate for young children, particularly for the conservative Christian audience the show was designed for. In "Forever, Amen", for instance, A boy blames himself for his mother's miscarriage because he wished he wouldn't have a younger brother. That's a downright tragic and terrifying idea for adults, let alone children.
Examples from the video series
The Scrappy: The actual animated show is this to the TV station Family Net nowadays, especially when in the 2009-2010 season, their Saturday morning line-up added Underdog and The Bullwinkle Show, but were dropped the following season.
The animated show can also be The Scrappy for fans of the radio show. The tone and quality of the animated series is vastly inferior to the radio show. You can tell that the creators don't have any respect for animation.
It no longer airs on Family Net as of October 2011... but they still air the Christmas Episode the Saturday before Christmas... at the cost of not airing the other shows on the line-up!