Air Force Museum at Dayton has both a YF-12A and the SR-71.
Great museum. They have several really unique items like the McDonnell XF-85 Goblin. Totally worth a trip out there and spend at LEAST a whole day there.
Another good one is the New England Air Museum in Windsor Locks, CT.
For a small privately run museum, they have a few really special items there as well like the only GeeBee Model A and the only VS-44A left.
www.neam.org. Their GeeBee R1 replica is unique in that they had access to the original plans to build it and the engine they put in it is very close by serial number to the one in the original. They made a promise to never let it be flown so they could use the plans. They even had pointers from the designer while they were working on it.
The Intrepid is good too. They have an A-12 there.
The Hiller Museum in CA is pretty neat too.
Hiller Aviation Museum Got a special behind the scenes tour with my Dad while out there for my brother's wedding and we went there on a lark. They weren't open yet, but one of the guys took us through it anyway since they were there working on stuff. Was cool.
Obviously, the Smithsonian Air & Space Museum is at the top of the pyramid. Just the part on the Mall is impressive, but I need to go back there and visit both there and the Udvar-Hazy location.