I'm rereading
Harry Potter and the Half-Blood Prince carefully, looking for clues about what's really going on. It's tedious work, and seldom leads to anything conclusive, but I'm sure Yeish Lanu Harbe Baquanim will agree that if I practise these skills enough, I could become a highly respected holder of a PhD in English literature. Here's what I've noticed so far. I'll try to stick to facts instead of the sort of unconvincing speculation the extended Maxiebaby clan found on the internet.
1. Notice that Tonks and Draco Malfoy seem to share quite a link. For example, Tonks rescues Harry after Malfoy freezes him under the Invisibility Cloak in the Hogwarts Express on the first day of school; Tonks shows up outside the seventh-floor (Canadian: floor seven) corridor adjoining the Room of Requirement, where Malfoy is supposed to be practising; Tonks and Malfoy both look progressively thinner and sicker throughout the book's dénouement. Could they be the same person? Lupin also looks worse as the book goes on; is that related?
2. This one is glaring, of course: some of what Dumbledore says in the cave between drinks from Voldemort's Horcrux-protecting potion sounds a lot like what Snape ought to say if he were reliving and regretting his betrayal of the Potter parents. Makes you wonder whether the Dumbledore whom Harry accompanies to the cave could really be Snape. Supporting this possibility is Dumbledore's blanching when Harry tells him he has discovered that it was Snape who reported Trelawney's prophecy to Voldemort (i.e., me); Dumbledore's asking Harry to fetch his Invisibility Cloak, when he had long before asked Harry to carry it with him always; Dumbledore's youthful physical abilities when he and Harry swim into the cave and when they fly back to Hogwarts; and Dumbledore's Snape-style healing of his own wound while in the cave antechamber. On the other hand, the real Dumbledore might ask Harry to fetch his Invisibility Cloak not because he thought that Harry didn't already have it, but because he wanted Harry to do what he knew Harry would do: alert Ron and Hermione as to what was transpiring, and possibly have them stand guard as they ended up doing.
3. Someone should do a really close study of what Dumbledore does with each of his hands throughout the book; there's a lot of seemingly gratuitous detail about which of his hands does what. Inconsistencies might prove revealing.
4. We never, of course, actually find out why Dumbledore trusted Snape so. That must certainly come out in #7. I think it will be revealed by Dumbledore, but, of course, it may be discovered in some other way.
5. Bellatrix and Narcissa go to find Snape in Spinner's End where, evidently, they understood him to be residing during the summer vacation. However, when Dumbledore injured his hand, which was shortly before he fetched Harry from the Dursleys' - i.e., in the middle of the summer, Dumbledore says he returned to Hogwarts "desperately injured," and was saved only by the expert ministrations of Snape, which presumably means that Snape was at Hogwarts at the time. I'm not sure whether this is in the least significant, but I wonder what Snape was doing at Hogwarts. Had Dumbledore summoned him there?
6. Maybe there's something wrong with Fred and George. "Crookshanks's yellow eyes followed" one of their fanged frisbees "and he hissed when it came too close" (Caput 9); "Crookshanks trotted after" Ginny, "his yellow eyes fixed upon Arnold" the Pygmy Puff (Caput 14), another Weasleys' Wizard Wheezes product. As we know from Book 3, Crookshanks is very good at detecting evil things, and he doesn't like them.
