I've got a 3 (girl) and 7 (boy) year old and live in DC. They're favorite places to go are (in order):

1. The National Zoo - It really can't be beat.
2. Air and Space Museum - I think it's dated, but the kids move it.
3. Natural History Museum - Dinosaurs and more
4. National Sculpture Garden (next to the Natural History) - lots of cool to touch and a fountain.
5. FDR Memorial - For some reason, the kids love this place

The best way to visit the museums is just to park near the Mall and walk around. Just break up the Mall into days. Day 1 is everything east of the Washington monument, Day 2 is west. There's lots of places to take breaks. it's really not a "haul" as another poster said.

Best place to eat on the Mall is in the Museum of the American Indian (next to the Air and Space museum). An unbeliveable cafe was interesting and kid-friendly food. Definitely beats the McDonalds in the Air and Space!

Other places the kids might like, but cost some $$ include:
- Spy Museum
- Newseum

The Udvar-Hazy is nice.. but waaayyy out there. Same with the Botanical Gardens.

Other possibilities:
- National Postal Museum (next to Union Station) - Some good exhibits
- National Geographic Building - they usually have a good exhibit or two there, but it's uptown a bit.

+1 for Theodore Roosevelt Island. Good place.

Good luck!