My favorites are the Museum of Flight in Seattle and the Smithsonian. I haven't made it to the new annex at Dulles yet. For a special treat, you can go to the Museum of Flight Restoration Center at Paine Field (Everett, WA) and wander around their warehouse and restoration center freely. Boeing keeps their mint 247 there as well.
The most disappointing aviation museum I've been to was just outside of Narita Airport in Japan.
The most disappointing aviation museum I've been to was just outside of Narita Airport in Japan.