I've been to quite a few, but there are a couple that I really need to get to yet (Pima and National Naval Aviation Museum).
Here's the ones I've visited:
SAC Museum: love the Snark and Atlas missiles out front, the B-52B, and all of the stuff stored out back (including a British Vulcan bomber).
Pacific Aviation Museum (at Pearl Harbor): love the B-17E they have. Would be nice to see it restored.
National Museum of the USAF: without question, the most complete museum for the USAF. Truly amazing and am looking forward to a return visit now that the 4th building is open
USS Midway (San Diego): Since I've yet to get to the National Naval Aviation Museum, seeing some 1950s/60s naval aircraft was pretty cool. Things like a Photo Cougar, Skywarrior, Tracker, Vigilante
USS Intrepid (New York City): Seeing an F3H Demon, FJ Fury, and E3 Tracer was neat and there's the Space Shuttle Enterprise (which I had seen at Udvar Hazy before they moved it)
Smithsonian Air & Space (on the Mall): I go to DC a lot for work, and I always carve out time to drop by. I basically know this place like the back of my hand and I love every moment I'm there
Smithsonian Udvar Hazy: What a great museum: tons of rare or one-of-a-kind items. Only been there twice so I need to get back...I just wish it was easier to get to (I'm never in DC with a car).
Minnesota Air National Guard Museum: I like 1950s jets, so any opportunity to see a Starfire or Scorpion is fun!