The original concept for Pajama Sam was a character known as "Pumpkin Head Boy" who, fittingly, had a pumpkin for a head. This was scrapped as it was believed that Pumpkin Head Boy games would only be able to move units during Halloween, despite the game not being envisioned as a seasonal title. This is referenced in Pajama Sam: No Need to Hide When It's Dark Outside, with Sam reading a book titled Pumpkinhead Boy: A Brief Tragedy about a boy with a pumpkin on his head removing his pumpkin due to concerns of seasonality. Notably, the story in the game alludes to a "lawsuit by that big guy in Atlanta". It is unknown if that is a non-sequitur or another part of the real-world Pumpkin Head Boy story that has not yet surfaced. Later, in Pajama Sam 3: You Are What You Eat From Your Head to Your Feet, Sam would wear a pumpkin on his head as a disguise at one point in the game.

Pajama Sam: No Need to Hide When It's Dark Outside and Freddi Fish and the Case of the Missing Kelp Seeds were released on the Wii as Pajama Sam: Don’t Fear the Dark and Freddi Fish: Kelp Seed Mystery respectively, alongside Spy Fox: Dry Cereal, which kept its name. However, these ports ran off of the ScummVM emulator engine and did not use proper attribution, leading to all unsold copies of the games being removed from sale and destroyed, and mandatory donations being made to the Free Software Foundation.