Richard and Tess, in addition to Le Vaudeville (in the Bourse) which I've mentioned,
there's Chez Julien (owned by the same people, between Republic and Opera areas). Both are old-time brasseries with superb food and a local crowd.
I don't know the name, but just as you cross the bridge from Ile de la Cite onto Ile Saint-Louis, there's a cafe to the left that serves wonderful choucroute and cassoulet, both of which are getting harder to find.
In the Saint-Germain area there are a lot of famous cafes, but the less famous Le Petit Zinc has wonderful food and a great terrace. Just politely refuse to sit inside! Next to the famous Brasserie Lipp, which I've heard is a bit snooty, is a little dive called Tavern Saint-Germain. The food is good and reasonable and the people-watching is fun. They do kareoki in the basement in the evenings which you can't hear on the ground floor, but the young crowd coming and going is fun to watch.
Don't miss the Luxemburg Gardens--the nicest park in Paris, I think. There's an adorable outdoor cafe there that's a nice stop for a drink or a snack.
Be sure not to miss the Au Bon Marche epicerie, an entire ground floor of the department store devoted to food. Plan to shop there for a picnic. It's between Saint-Germain and the Orsay, and sure to be listed in the guide books
NFR tip: Buy a museum pass. Not only does it pay for itself in 2-3 museums but you get to skip the lines and enter at the group entrance. With DaVinci Code mania in full swing you'll save many hours!
I never would have thought to eat at the top of the Montparnasse Tower. That thing is so ugly it would be worth it not to look at it. Great idea, Gretchen!