These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Best Boss Ever: The dual Scarab battle on The Covenant. Probably the coolest battle in the series.
Best Level Ever: Most players would nominate the entire second half of the game for this- with the notable exception of Cortana.
Then "The Covenant", where Master Chief and a small army takes out two Scarabs. And there are not cutscenes for that, you have to pilot something onto the backs of those things and blow them up yourself.
The Storm is the best level in the first half.
Complete Monster: Truth is far beyond redemption by this game, being quite willing to wipe out all life in the galaxy just to be viewed as a god.
Crowning Moment Of Awesome: The level "The Covenant", where you get an amazing shot of a battlefield you're about to be in (complete with two Scarabs and a whole lotta Banshees!) while having a lovely Crowning Music of Awesome.
Master Chief: You know me. When I make a promise...
Cortana:...you...keep it. I do know how to pick 'em.
Fridge Brilliance: Cortana says the reason she chose Master Chief over every other Spartan is luck. Check out what happens to Noble Six, a SPARTAN who is as equally skilled as John, in Halo: Reach, and her statement reverberates in hindsight.
The policy of the military is that SPARTANs never die, they are just listed as MIA. That's exactly what happens to Chief in the most literal sense.
Fridge Horror: If Gravemind wasn't in such a hurry to get to the Ark, the Flood would have had plenty of opportunity to infest Earth and wipe out what little remains of humanity, leaving the Chief and company backing up a graveyard while they were preoccupied with Truth.
Well, they did try to, dropping off an infected Covenant cruiser in Voi, which would have quickly taken over the entire planet had it not been for Half-Jaw glassing the immediate area before anything could escape.
Fridge Logic: Even had Truth succeeded in firing the Halo rings, he wouldn't have been able to kill all life in the Galaxy as the game implies - without Installation 04, there would have been a huge gap in the Array's firing coverage.
The Arbiter's refusal to believe that Master Chief is truly dead.
The final line of the trilogy: "Wake me... when you need me."
That One Level: For many, Cortana, particularly if on higher difficulties and god help you if you're doing it alone. If there's anything worse than Flood rushes plus endless needle death spamming your shields from Flood turrets beyond easy range of your weapons plus the walls being full of Infection Form pods that will pop open at a single stray shot, and thus re-animate all the Flood you've already killed behind you...
The real reason "Cortana" is hell, aside from having the same problems as The Library: When you are playing the level, both Cortana and Gravemind like to have moments, where everything slows down as you hear them talk. The dialogue just turns the entire level into one giant Mind Screw.