I love every aviation museum I've visited. My list includes, in no particular order:
The Polish Aviation Museum in Krakow - a little dark, but full of unique aircraft
The Royal Thai Air Force Museum in Bangkok - loaded with one-of-a-kind aircraft
The Evergreen Aviation Museum in Oregon - also loaded with one-of-a-kind aircraft
The Museum of Flight in Seattle (and restoration center in Everett)
The National Air & Space Museum (mall and Udvar-Hazy) - dark and tripods aren't allowed, but full of aircraft
The US
AF Museum (or whatever they call it now) - crowded and dark, but great
The Pima Air & Space Museum
The Israel Air Force Museum
The Tango Squadron in Chiang Mai
The RAF Museum in Hendon
The Fleet Air Arm Museum in Yeovilton
The South Kensington Science Museum in London
The Turkish Air Force Museum in Istanbul
The San Diego Aerospace Museum
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Photo © David Lednicer
The Milestones of Flight Museum in Lancaster
The Western Aerospace Museum in Oakland, surprisingly full of light
The Hiller Aviation Museum in San Carlos - a little dark and crowded, but great
The Olympic Flight Museum in Olympia
The Cavanaugh Flight Museum in Addison (Dallas)
The Vintage Flying Museum in Fort Worth
The Commemorative Air Force in Atlanta
The Intrepid Sea-Air-Space Museum in NYC
The Planes of Fame Museum in Chino
The March AFB Museum in Riverside
The Vietnam Air Force Museum (and other museums) in Hanoi
The War Remnants Museum in Ho Chi Minh City (Saigon) - kinda small
The Yankee Air Museum in Ypsilanti
The Air Force Flight Test Center Museum Airpark at Edwards AFB
The Plant 42 Heritage Airpark in Palmdale
The Tillamook Naval Air Station Museum in Tillamook - very dark
The Glenn L. Martin Aviation Museum in Middle River
The EAA Airventure Museum in Oshkosh
The Kalamazoo Air Zoo in Kalamazoo
The Alaska Aviation Heritage Museum in Anchorage
Wally Fisk's collection in Minnesota - I don't think its open to the general public any more
The Fighter Aircraft Museum in Mesa - now moved to the Museum of Flight in Seattle
The New England Air Museum in Windsor Locks
The Museum of Science and Industry in Chicago - small, but where else are you going to see a real Stuka?
Grissom AFB Museum in Kokomo
The Canada Aviation Museum in Ottawa
The British Columbia Aviation Museum in Sidney
Ones I've missed:
Kbely outside of Prague - forgot to schedule it in
The Republic of China Air Force Museum in Taipei - had to catch a flight and ran out of time
Vigna di Valle outside of Rome - had it scheduled, but lacked transportation
Coming soon: I should be visiting the Chinese museum in Datangshan in May...