I almost thought that Sam could develop somewhat psychic use of the toys given his exposure. However, it seems unlikely that Sam or Skunkape could use them on their own. In 301 its explained that Skunkape used Gordon the Alien Brain to use the toys, and Sam is able to participate because he is Max's partner. Although its never really explained how Sam can join in powers like future vision, when he and Max aren't touching.
And to clear the matter up for those on this forum, this picture shows the supporting cast of Season 3, not necessarily villains:
http://i28.tinypic.com/292xmp4.jpg
From left to right we have the molepeople family from 302, Baby Amelia Airheart, Girl Stinky, Sal, Paperwaite/Dr Norrignton/Yog Soggoth, Skunkape, Nicolas St. Kringle, Momma Bosco, Grandpa Stinky, Charlie Ho-Tep, Samulacra, and giant max legs.
Now, Momma Bosco looks weird, almost like Brady Culture, since she's never worn shorts in any of the games. And the giant legs are probably from the giant Sammunmak statue from 303. Although why those are in the picture are anyones guess, since they didn't do anything in the episode. If those were from monster max the legs would look at least amphibious to follow the rest of his transformation.
The season is called The Devil's Playhouse. While this could refer to the locations in the game where The Devil's Toy box is used I suspect this is more or a separate location. That's why I think Beelzebub may make a reappearance. One of the random lines when talking to Max in this last episode goes along the lines of "Sam: If this is The Devil's Toy Box, how come we haven't run into him yet? Max: His agent's probably holding out for more money" Beezlebub is the Devil in the Sam & Max games. Also, at the end of 205 Beelzebub ominously predicts that he will meet Sam & Max sooner than they think. While that could refer to his appearance during the wedding scene in the credits, his tone is far too wicked. Besides, all the season characters minus the true villain appear in the credits sequence. Also, Beelzebub and The Narrator seem to speak with the same accent, though I don't know if they share the same voice actor.
Outside of this prediction, I doubt any of the suspected characters are dead. The characters always persist even if they're technically dead, like previous seasons villains in Hell.
And the Toys of Power still linger in some ways. They've been used during the whole season. Max has achieved his full potential. The Chthonic Destroyer seems to "destroy" things from the Dark Dimension by returning them there, so they would still exist in a different dimension. For example, since the Toy Box was sent to "our" universe the Chthonic Destroyer has existed in that other dimension when not in use. All this highly suggests a visit to the "Devil's Playhouse" location or the Dark Dimensions.
The biggest question I have unanswered from this last episode is: How exactly did Charlie Ho-Tep come to life and get a sample of Sam's DNA for cloning?