Antique Automobile Club of America Museum
Nifty car museum in Hershey PA. They regularly have special exhibits, so it's always worth checking out their web site. Last one I saw was a Lotus exhibit with couple dozen Lotus cars of all types.
American Helicopter Museum and Education Center
Helicopter museum in West Chester PA. Camera wasn't the best, but was a nice smaller museum. They have a dozen full helicopters and lots of other rotor aircraft. They have an V-22 Osprey on display. I worked for a company (later bought out by Sikorsky) that was started by the same guy who helped create the museum.
Andy Warhol Museum
Prepare for a lot of stairs, it's seven floors tall. Two or more of the floors have visiting artists, which vary pretty greatly. There's a lot of Warhol's iconic work. Well over $55 million pieces of Warhol's art.
America on Wheels Museum
Usually have about 80 cars on display. Including a large number of Mack trucks. There's also the 1889 Nadig Gas-Powered Carriage, one of the first gas powered vehicles ever created. They have a good section on alternative fueled vehicles.
Visited with a buddy to find the Delaware and Hudson Gravity Railroad. Coal went downhill by gravity alone. Empty cars were wenched uphill. It was in operation for 70 years (1829–1899). Made for an awesome walking trail as it was so carefully leveled.
Philadelphia Museum of Art
240,000 pieces of art on display. Modern art section is always terrible, but the rest of the museum is probably the best art museums I've ever seen. They have rotating visiting exhibits. There's several annexes including the Rodin Museum, which has the largest collection of his works outside of Paris. Including the Thinker, his most well known sculpture. There's also the statue of Rocky.
Rough and Tumble Engineers Historical Association
They call themselves a living museum, and they're not kidding. 33 acres of steam engines, early farm tractors, massive stationry engines, full sized working saw mill, threshing machines.