Hierarchies and trees are ubiquitous in Computer Science and Software Engineering. Examples include:
file systems
organizational hierarchies
partonomic hierarchies
accountability hierarchies
taxonomies
genealogies
outlines
search trees
parse trees
Here's an example of a partonomic hierarchy:
Package
Class
Method
Statement
There are several design patterns that are often associated with hierarchies:
The Visitor Pattern
The Interpreter Pattern
Many of these patterns can be seen in the Alpha Interpreter.