User blog comment:AwesomeIsMyName/The Last Episodes of Mystery Incorporated Discussion/@comment-7735323-20130408220958

Mine are:

Bold text Beware the Beast from Below, The Legend of Alice May, Mystery Solvers Club State Finals, Escape From Mystery Manor, The Dragon's Secret, Menace of the Manticore, A Haunting in Crystal Cove, All Fear the Freak, The Night the Clown Cried, Part 1 and 2, The Midnight Zone, Dance of the Undead, Stand and Deliver, Nightmare in Red, Dark Night of the Hunters, Gates of Gloom, Through the Curtains and Come Undone.

I have choosen these particular episodes because of the exciting storylines, interesting characters and important milestones, such as the first and last episode. A small selection from both seasons, however these (for me) are episodes that really stand out.