Susan and Monte,
I agree with the Musee d'Orsay lovers. Absolutely incredible building as well as all the paintings you have ever seen in the coffee table art books. Degas' little dancer with her tulle skirt. I also love the Louvre, although it is really crowded and very hot (in summer--not sure when you are going). I was with my small son, and he took his 7 year old self from one floor vent to the other--and THAT is what he remembers from the Louvre. The Musee de l'Armee Invalides is also cool, especially if you are tired of art (which does happen). Napoleon's tomb, and fascinating military museums dating to the 13th century.
Sainte-Chapelle and the iles are actually my favorites of all, both "museums" and neighborhoods, and the Marais is also great.
If you take one of the bateaux-mouches at twilight (rather than full-on night), your photos will be suffused with a beautiful rosy glow, and you'll swear you found la vie en rose for real. :) AND, if you afterward go across the Seine to the Trocadero/Palais de Chaillot, you will have the best view of the Eiffel Tower at night in all of Paris. Speaking of the Eiffel Tower, I assume you are speaking of a 5:00 reservation, which is by far the smartest move we made the last time we were in Paris. You can do it online.