Personally, mine is the whole tragedy of the Forerunners. Tragedies always just carry so much emotion with them, and I love a story with good drama. What's more dramatic than a story in which you know an entire galaxy is going to be wiped clean of all sentient life?
I don't care if it's from what we got in the Halo 3 terminals, the Halo 4 terminals, Halo Legends, or the Forerunner trilogy. I think they all express the emotions behind the story from a psychological perspective equally well.
Getting to see the Librarian and the Didact slowly torn apart by their commitment to their responsibilities in the Halo 4 terminals was absolutely terrible, because you could see where they came from and where they ended up. The final communications between Librarian and the Iso-Didact in the Halo 3 terminals, and just the whole arc from the Forerunner trilogy. This progression from overconfidence, slowly decaying into ultimate defeat from which there is no escape... It reminds me so much of the staple scenario from zombie fiction "I'm bitten, I know I'm going to die and turn... how do I handle that emotionally and within the larger context of the group I'm with?" It's a similar 'damned if you do, damned if you don't' kind of thing. Frequently I find myself wishing I could have many of my friends and family who aren't interested in Halo read through just those three books. But I know that a lot of its impact will be lost without further context and investment in the universe, and it would of course ruin the plot twist for any who might still play the first game.

After posting my last thread about headcanon, I really saw even more how varied our enjoyment of the fiction really is. Some people (like myself) try to take everything that is given to us and make it work within the fiction as best we can, while others just flat out ignore certain parts of the fiction that they don't like... and everything in between. I think it's interesting what sort of stories people like and don't like, and the lengths they do or don't go to to enjoy those wholly.

So this just kind of led to me wondering which specific story arcs within this widespread universe appeal to people. Personally, my second favorite is Human Weakness, from Halo Legends. I love the real psychological development going on there, and the basic arc of Cortana's fight against the Gravemind.

So what's yours? :)