I made this list in another thread but I'll do it again.
My favorite levels in order are:
1. Halo
2. Silent Cartographer
3. Two Betrayals
4. Assault on the Control Room
5. The Maw
6. Truth and Reconciliation
7. The Library - Like V3rin said, I LOVE the atmosphere in this level.
8. Pillar of Autumn
9. 343 Guilty Spark
10. Keyes - This is the only level I really don't care for.