It's always amusing when devs kind of know you're going to cheat with a game. I believe there are a few hidden weapons in FFIV and The After Years that were dummied out. If you hack the game to put them in your inventory, their description pretty much says "You must be an elite hacker to have this!".

The MegaTen devs occasionally put in game-ending bugs into their games that activate when it realizes it's being played on an emulator.