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If you haven’t read "The Half-Blood Prince" then stop reading

now, for spoilers await ye’ with nasty sharp pointy teeth.

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Aunt Petunia is a witch (certainty 60%)

• We already know she’s been in touch with Dumbledore, possibly more than once. 
• She knows waaaay too much about the wizarding world. 
• She shares a bloodline with Lily Potter, and according to J.K. Rowling’s OWN FAQ she is not a Squib.

So, if she’s got magic parents, and she’s not a squib, then she must be a witch.  Why then, is she living as a muggle?  I think she’s perhaps sworn off magic in an effort to hide out from Voldemort, or at least not draw attention to herself.  Perhaps she even had her memory modified so that she wouldn’t know she was a witch, but over the years her memory is repairing itself.  Who knows?  The important thing is that you can logically conclude that she was a witch.  Now it’s possble that she’s only Lily’s HALF-sister, and does not in fact have any magic parents, in which case my theory is shot.  Since we know that Lily was called a "MudBlood" by Snape from his own memory in the pensieve, we can assume that one of her parents was a muggle.  It’s probably in there somewhere, but I’m not sure off the top of my head.

CORRECTION:
After some minor amounts of research on a couple of fan sites, I see that Lily was muggle-born, so BOTH her parents are muggles.  But there must be some wizard blood in her history SOMEWHERE for her to be a witch, so maybe Petunia has it too.  We’ll see.

Dumbledore is alive (certainty 80%)

• Dumbledore’s too smart to trust Snape without a pretty f’n good reason.
  Everyone in the world thinks Snape’s a sleaze, but Dumbledore won’t here a word of it.  Also McGonagall said that his reason was "ironclad" although she did not know it herself.
• He completely froze Harry rather than telling him to hide.
  If Dumbledore didn’t KNOW ahead of time that things were going to get "weird", he wouldn’t have frozen Harry, but simply would have silenced him, or TOLD him to remain quiet while he talked to Malfoy.  Certainly in the time it takes to utter "Petrificus Totalus", he could have said "Silencio" much more easily.
• Wizards have faked their own deaths before.
  If Pettigrew could do it, then certainly Snape and Dumbledore could pull it off together.
• Broken spells
  If Dumbledore’s "Petrificus Totalus" spell abated instantly on his "death", why do the death eaters still have to run to the edge of the grounds before disapparating?  Now this isn’t a very strong argument, since you would expect the castle enchantments to be of a slightly more permanent nature when cast.  It doesn’t actually do a lot of good to put up protections if all it takes is eliminating a single person to disable them, but I thought I’d mention it anyway.
• New concepts in this book.
  To take a jaded, analytical look at things:  Why introduce the entirely new concept of non-verbal casting in this book if it is not of some importance to the story?  Also the idea of the Horcrux.  It’s essential to why Voldemort is immortal, but could also just be handy enough to save Dumbledore’s butt, right?  You have to commit murder to create one, but who says you can’t "Save" the sould you’re killing at the time, eh?
• Snape’s combination of abilities.
  Snape is an "Accomplished Occlumens", able to hide his thoughts from even the other teachers and Dumbledore himself.  So he may just be the only person we know of capable of casting one spell non-verbally while speaking the words to another spell, and NOT being detected by those around him.  Snape’s ability as a "legilimens" would have let him read Dumbledore’s thoughts at that critical moment so that Dumbledore could tell him "Do it now!" without having to use some sign or code-word that might have seemed suspicious.
• And the really jaded answer.
  It’s no fun to have the guy you’ve hated through the whole series turn out to actually be a bad guy, is it?  Where’s the twist in that?  Where’s the intrigue?  Rowling is FAR more interesting than that.
• But what about the new portrait in the headmaster’s office?
  No-one has ever said that the portraits are only of dead people, and he did have a chance while Harry was off retrieving his invisibility cloak to have set up the painting himself, knowing that this was the night he must disappear.  It could very well be that the portraits exist throughout a headmaster’s tenure so that they may observe and remember the things he’s done.  Also, that portrait never speaks.  It could very well be a moving picture like those in the Daily Prophet, couldn’t it?  And again with the jaded analytical argument.  McGonagall makes what is only described as an "odd movement, as if steeling herself" when she sees the new portrait.  It’s not like Rowling to barely describe things like that unless she has a very good reason for it.

I’ll add more as I think of them, but these are the two most interesting areas of thought for me right now.