In Episode 5, the music that plays when Strong Bad's house is being haunted by ghosts sounds extremely similar to the Ghost House theme from Super Mario World.
A shirt normally unobtainable during Strong Badia the Free, Baddest of the Bands, and Dangeresque 3: The Criminal Projective can be accessed by adding the 32-bit value "shirtmuscles" to the game's registry. It even has its own dialogue when Strong Bad puts it on. The shirt is a refrence to the Sbmail "tanning" where Strong Bad invents a device to draw abs on their body called the Ab-Abber 2000
According to some unused voice clips, there was originally going to be a costume sharing feature which would allow the player to trade their acquired costumes with other people who played the game.