(Spoilers for Possibly Everything) Manipulation and Time Travel
 

Trawling TVTropes, I found the following comment on the Characters page for Sam and Max:

Granted, the text in question came with a hyperlink to the Player Character page, but perhaps... just perhaps... it's more than that. Perhaps Sam was so easy to control, perhaps he seemed almost made for it... because he was?

What if Sam were actually one of the Dogglegangers, turned into a child and sent back through time to get adopted, meet Max and grow up alongside him, thus ensuring his own creation? That would explain why Sam seemed so easy to control--he was created to be controlled by the very being who would later control him.

(I also heard about one of the clones hugging a stuffed rabbit or something. If he somehow survives, he'd make an excellent candidate for truly being Sam)

Now to see if I can make everything in Chariots of the Dogs make sense--such as Present Sam and Present Max somehow knowing they'd have to get to the moon as far back as Situation: Comedy, as well as depriving Past Sam and Past Max of the recording contract they'd need to get onto Myra's show.

This is going to make my head hurt.

If I remember correctly in episode 305 it's Momma Bosco who makes that comment about Sam being easily controlled. I wouldn't read too much into it, it's probably just some kind of meta-joke, because you the player are controlling Sam all the time. But of course you're free to speculate.

Maybe, but Charlie Ho-Tep also says that about Sam, saying that it's WHY he chose to make a thousand clones of him. All of them are going to sacrifice themselves to Junior, and the last thing Charlie Ho-Tep needed was an angry clone-mob.