First time going? Going with kids?
My favorite museum in Paris is the Rodin museum. It's a nice respite from all of the activity around the city. Easy to get into and has a nice outdoor cafe to have a relaxed lunch.
Agree somewhat with PW on the Eiffel. If you've already done it, probably not worth the hassle. They've put up a bunch of barriers, presumably from the Olympics. It was already a pain to get out there and it only makes it worse to navigate once you're there. If you want to do some wine and cheese on the mall in front of the tower, that's always nice, but not much need to go up it.
St Germain/Latin Quarter are my favorite areas. Fun to walk around. Feels more local than the main touristy areas. The Marais is great to walk around as well.
As far as food, Frenchie is excellent and we had a great meal at Pink Mamma's when we were there last month. There is a speak easy in the basement for a pre or post drink.