I have too many to choose from, so I'll just pick from the list you provided. First Strike has to be one of my favorite books in the series. I played the games long before I read the books, so getting to read First Strike and learning about how Johnson and the Chief actually got back to Earth (which the armorer in Halo 2 specifically asked about) was a real treat.
I love how Bungie would prioritize game lore over extended lore, but would still add in little moments like that for us lore fans. While I definitely appreciate 343's approach that puts all lore on equal footing, moments like that showed me that Bungie still cared about the extended lore, even if they were willing to retcon extended lore in favor of game lore.
Not to go beyond your thread topic OP, but I think 343 could learn from that approach. With them trying to make Infinite a simpler story for more casual fans, moments like that from Halo 2 were great examples of meshing extended lore and game lore without losing casual fans in the minutia of the extended lore. Those who read First Strike knew all about how Johnson got back from Installation 04, while casual fans could just accept the "it's classified" response at face value.