Simply put -- when you need to navigate between more than 2 directories, usually several times, as cd - just won't do with the 3rd+ folder.
So, instead of trying to come up again with long paths by looking at your buffer's history or tab-completing a long pathway (for example, in a new directory structure you just met, like a .tar.gz archive) you simply stack the important ones up as you go and if needed you conveniently move to them by their number alone. The interface also allows you to re-order them or pop out the ones you don't need.
Directories stacking can also be used in scripts similarly for operations that span several directories. Rotating among complex directories becomes slick and swift.