Musee D'Orsay was wonderful! Also, L'Orangerie museum is right by the Louvre and has Monet's original water lilies and a really cool impressionist exhibit. I also really wish that I had gone to Monet's garden at Giverny (it's a short train ride out of the city) which is the place he painted all of those water lilies with the bridge that is in so many of his paintings. Versailles was really cool, too, but I would try to go not on a weekend or really tourist-heavy day (if such a thing exists) because it was so crowded that I couldn't really enjoy the inside.
In London, I really liked the national portrait gallery, and if you are a Harry Potter fan it takes about 3 seconds to go to platform 9 3/4 in King's Cross and St. Pancras is where the car flew around in the 2nd movie, right across the street. Also over there is the Library, which is really cool also. They have the original Magna Carta and the original Beowulf and some other really cool things. I would also try to go to high tea and the theater, both of which are so much fun! The British museum is AMAZING and has soooo much cool stuff in it you could spend an entire day there. There is also a veterinary exhibit in the Science and Industry museum (? maybe natural history?), but it was closed when I was there. If you want to get out of the city you can go on tours of James Herriot's house and Darwin's house, both of which are within a couple hours train ride I believe. I didn't get a chance to go to Herriot's, but I really wanted to!