We're nearing the end of the time I can meta on this: I've said (oh, how I've said) that Snape's loyalty to Dumbledore isn't remotely in question because of the structure of Book 6 and the series as a whole, and that I dislike how Harry's been left in the dark at the end of Book 6, since it's unfair to make the answers plain to the reader but leave the protagonist unenlightened at the conclusion of a volume. (To clarify, this does not mean that Harry is stupid not to have seen it--Harry didn't get to read the Spinner's End chapter.) But here's another way that cheats us: do you realize, if Snape's motives had been revealed to Harry--if Snape or a glimpse into Dumbledore's pensieve or his will or what have you had communicated this to Harry at the end of Book 6, and Harry as well as the reader saw that Snape had gone into deep cover at Dumbledore's command--does everyone realize that that ending would actually have made Snape's ultimate loyalties ambiguous? That the "is Snape good or is Snape evil?" stickers and debates and contests would actually have had meat, if that had occurred?
Seriously, a third of us would be saying, "Snape killed Dumbledore at Dumbledore's command; we now know that the last book will be about Harry and Snape being on the same side, and if they will triumph over Voldemort and live." Another third would say, "Snape's pulled the wool over everyone's eyes--Dumbledore thought Snape was reluctant to kill him, but in reality Snape's been on Voldemort's side all the time, and just wait until Harry confronts Voldemort expecting Snape to have his back and Snape starts to laugh, 'What, you didn't believe that claptrap I told you, Potter? I've never been so delighted to cast a spell in my life as the day I killed that Slytherin-hating old fool.' It'll be amazing!" And the last third would still be insisting, "Snape is his own man, and his actions at the end will do what is best for Snape."
Another reason to resent the ending of Half-Blood Prince. I would have loved seeing all the sides of that debate.