(Searched for "Halo" and got two unrelated threads)
I just finished Ghosts of Onyx a couple days ago, and was hoping other people on CGR had read at least two or three of the Halo books.
I imagine there are people who would scoff at these after seeing them in bookstores (or somewhere else), but, like any video game with a great storyline, you can't contain or explain everything in three video games (that I believe span about 30-40 hours of game time). There's a lot of stuff that happens before the first game, between 1 and 2, and between 2 and 3 (Essentially, Master Chief is not the only character facing problems).
Anyways, in the hopes that there's some discussion, I'm going to rank the books (minus The Cole Protocol, which I haven't read). I noticed that Eric Nylund writes my favorites.
The Fall of Reach - The writing and characters seem to be most interesting here, and I loved reading the rich back-story. It also focuses on Dr. Halsey a lot, and I think she's my favorite character in the whole series.
Ghosts of Onyx - The Spartan-focused story is probably why I liked this one a lot, and it has more of a suspenseful feel compared to the others (where you sometimes know what's going to happen). The ending is also related to the third game in a very important way.
First Strike - Nice way to bridge the gap between the first and second game. Not much else to say about this one.
Contact Harvest - Sergeant Johnson is an interesting character, and first contact with the Covenant is interesting, but there's a bit too much focus on two AIs who run Harvest.
The Flood - Pretty simple why I liked this one the least - it follows the first game, and even an amazing author isn't going to be able to save it from getting pretty repetitive. Not to mention you'll probably remember what's gonna happen next for most of the book.
Lastly, I'll add this very handy timeline which details everything from well before first contact with the Covenant up to the end of Halo 3:
Halo Story Page | Ancillary | Halo Story Timeline