We have crates in the basement along with emergency food, water, leashes, and first aid stuff. The cat is confined upstairs, where there is an additional crate for him. If I'm home, the dogs wear their collars during tornado watches (they don't wear them at home usually) and I'm very aware of storms. We would have a good amount of warning in case of floods, and our house is actually on a high enough hill that it has never been underwater, even in the flood of '93.
That's a good idea, to train them to go to the door when the fire alarm goes off.