They were folders named the characters' names. I don't know if they were in with the other characters or what, ask a hacking pro to explain that part.
They could've been on the disc for any reason whatsoever, but that's just being overly pessimistic. I'm a pessimist, but I'm at least going to speculate instead of saying "They mean nothing unless Nintendo says something." I mean, where do you get with that?
The characters are
Mewtwo
Roy
Toon Zelda
Toon Shiek
Dixie Kong
Dr. Mario
Plusle & Minun (This is speculation, the file was named "prai_mun" or something)
What else do you possibly think they could BE? I mean, I might say they could've downgraded the three clones to PokeBalls/ATs, and Dixie and P/M as well, but Toon Zelda/Shiek? Seems too likely as a character.
Also
http://www.gamespot.com/wii/action/supersmashbros/show_msgs.php?topic_id=m-1-41478260&pid=928518
It says they're on the debug menu. If they're on the debug menu, chances are they're in the section for characters. If they're in that section, they kind of...have to be characters.