It depends on the local environment, but for alpine areas, in the vestibule works well. Damp, muddy boots don't go so well with sleeping bags and other gear and bags that will really contain the dirt also tend to contain the moisture more than desired. The desert might call for something different if you actually brought a tent (never have-carrying water was enough weight). If foxes or coyotes are a problem, then making boots nonportable is always an option. A mosquito net would keep out the 6 and 8-legged critters without hurting airflow too much or adding weight to the load.