GoT centers on some mysteries, some of which are explained and some of which are not. These mysteries are:
1. Who killed Jon Aryn? All fingers point toward the Lannisters (Cersei, et al). Jon had figured out Joffrey was not Robert's child and was going to go to the king with this info, so they had him killed. But what of the (mis)information that Jon's son Robert was supposed to be fostered with Stannis at Dragonstone instead of with the Lannisters? That comes up a couple of times, but I'm not sure what to make of it.

2. Who gave the guy the knife to kill Bran? It's Littlefinger's knife, but he claims he lost it to Tyrion, which Tyrion denies. Was it Cersei? Did she hope to kill Bran and goad the Starks into war? Or was it Littlefinger? It's the attempted murder of Bran that sets the whole war into motion.

3. Who were the guys Arya overhears in the dungeon and what are they planning? They seem to be Illyrio and Varys, but I'm not sure. What are they up to? Are they conspiring to put Daenerys on the throne? If so, what's Varys' role in everything else that follows?

I'm also wondering about the idea of "honor" and what Martin is trying to say about it. Ned is, ostensibly, the most honorable of the characters, but that gets him and his family into all sorts of trouble. He eventually gets killed for it (though, interestingly enough, only after he "dishonors" himself by publicly lying about Joffrey's parentage). The death of Ned is the death of the traditional fantasy hero, I think. Jon is the other "honorable" character, but central to his conflict is what the honorable thing is. Is it helping his family or upholding his vows to the Watch? We know in later books he breaks some of his vows by riding with the wildlings and taking one as a "shield-wife", but he then breaks those promises and goes back to the Watch. Jon, who is the easiest character to like, shows the conflict between honor and fairness, or honor and "what's right." It's hard to criticize Jon, even when he breaks his vows. He also demonstrates the most growth in the first three books. Tyrion is another sympathetic character who is frequently "dishonorable" but often does "what's right." You can see some of the same elements in Daenerys' journey. As she becomes more self-confident, she strays further away from traditional notions of honor (either Westero's notions or the Dothraki ones) and more toward guiding herself and doing what is right. Jamie is on the same path beginning in the second book. Come to think of it, all get put on that path of growth by losing something important. Jamie loses a hand, Dany loses two families, Jon loses Winterfell and that family. Tyrion is in a constant state of loss due to his stature.

I know I am rambling a bit. In fact, I should probably stop my lit crit of the Martin series and do some actual work. I'm interested in what others think, though.