The Brothers Chapman like to hide various little extras in their skits, often at the end. Many Strong Bad emails have little extras, as well as the feature scenes like "Parsnips A'plenty" (Which features a scene of Strong Bad in hell saying , "Curses! I've gone to hell! How unfortunate!" — Click the "D" in 'The End'). I've found that a good way to find these extra scenes is to click somewhere in the movie and hit the tab key to look for clickable regions that aren't an obvious control.
Some of the extras are very impressive, including small atari-like arcade games, extended scenes, or, in one case of a Strong Bad email that I can't recall the title of, several minutes of audio. If you're watching Homestar Runner stuff and not getting these extras, you're really missing out.