Some nice Picasso and Casas in a special exhibit on the development of modern art in Barcelona.
A huge portrait of Lavoisier, by David. I am in such fanboy mode over this painting right now. (It's really big. And science-y. And they're so cute together! Stupid French Revolution.)
A few very science-fictional pieces by Yves Tanguy in the modern art section.
19th-century graffiti on the Egyptian shrine they've rebuilt in a gallery.
Musical instruments! They had a complete pipe organ by an early American craftsman, some early brass instruments with finger-holes, and neat wooden bells from Africa. The bells were arranged with one on each end of a handle so you got two working at once, and they had a four-way variety as well. (There might be two clappers in each bell as well--- this is as close as I could come with a quick web search.)
Another special exhibit was on Venice and the Islamic world. They had a Qu'ran printed in Venice, among the first printings ever! (The exhibit noted that printed Qu'rans reallyu didn't catch on until the 19th century.) There was also a few paintings which showed how much detail the painters had put into getting authentic Ottoman dress--- and then they used it to show Ottomans (rather than Jews) stoning St. Stephen.