Most emergency and rescue organizations strongly urge against ever leaving pets behind during a disaster. While there might be a temptation to believe it's better to just let them "ride out the storm," unfortunately, the duration of a crisis can be hard to predict. Should a situation take a sudden turn for the worse -- for example, your area becomes flooded, preventing you from returning home -- your pet's chances of survival will decrease significantly.
However, if you're faced with a situation where there's no choice but to leave the pets behind, FEMA recommends leaving them loose inside your house (as opposed to crated), along with access to an ample stock of food and water. Outfit your home with external notification stickers that alert outsiders that pets are inside (many organizations such as the ASPCA provide such emergency alert stickers for free or a nominal donation) and add additional signage as well. Of course, return as quickly as possible to your residence to ensure pets are accounted for and secure.