Well, I'm LTTP regarding Halo:CE levels, but I'd say that Halo and truth and Reconciliation are my favorite levels in the game. Halo's setting really blew me away at the time (it still does, actually), there was no whiff of repetetiveness, it had a good deal of variety (up-close action, sniping, fighting alone, fighting with a team, exploring in the 'hog for the first time,) and it was fairly open-ended as to which encounters you approached and in what order. Definitely the level that made me fall in love with the series, and probably my favorite level out of the game. Truth and Reconciliation drags a bit once you get inside the ship, but the on the ground portion is some of the most amazing combat in the series to date, and the setting was interesting as well. The series never topped that in terms of sniping missions.
The Silent Cartographer, Keyes, and 343 Guilty Spark are quality levels as well. The beach landing in Silent Cartographer was one of the most memorable parts in the game, and replaying it really makes me wish that Bungie had done a beach landing in New Mombassa in Halo 2 like they'd originally planned. Keyes is another quality level, the 3-way fights were some of the most intense in the game, and the escaping in the Banshee in the end was a really cool moment. The last half of the game is pretty much completely going back through where you were in the first half of the game, but I thought that Keyes was one of the only retreads that was really interesting and showed a compelling difference as to what the area was like before and after the flood escaped. And 343 Guilty Spark wasn't one of the best halo levels combat-wise, but the reveal of the flood was really well done and memorable, and the lead up to the reveal gave you a sense of dread that I haven't felt in games since, except for in Half-Life 2.
The Pillar of Autumn was such a throwaway level, I'm not even going to go into it. Just an all-around average level, didn't indicate at all what a great game was ahead.
Assault on the Control Room and its' sister level, Two Betrayals, are fairly good levels in a really cool environment (love the snow,) but they both drag on for too long and get too repetetive during the on-foot sections. The vehicle areas were a blast, though.
The Library is undoubtedly the worst level in the game, and the second-worst level in the series. It completely killed all the momentum and excitement the player had in the game by making you trek through identical hallway after identical hallway. Such crap.
And finally, The Maw. What's really over-looked about The Maw is how average it is as a level until the warthog run. It's very linear, enemies are just sort of thrown at you, and the encounters are just all-around unexciting. But the setting, amazing music, and incredible ending make me forgive The Maw for nearly being forgetable.