Categories of Controlled Vocabularies
Ironically, terminology about controlled vocabularies can be somewhat confusing. Much time has been spent understanding the differences between the categories of controlled vocabularies, and necessary conditions for each category. Of course, if you're reading this guide, you probably know this first hand. In general, there are three broad categories of controlled vocabularies: flat, multi-level and relational. Within these three categories, there are a variety of types of controlled vocabularies.

Flat Vocabularies
Authority File * Glossary * Dictionary * Gazetteer * Code List
All flat vocabularies contain a label and a value. These lists match the acceptable values with the appropriate metadata label. Some flat vocabularies will build upon this foundation, and add a definition or additional information about each value. These types of vocabulary really put the focus on the values only. No relationships are established, no hierarchies are setup, and no complicated matrices are necessary. Flat vocabularies are sets of three or four pieces of information - a label, a value, and possibly a definition and/or additional information.
Multi-Level Vocabularies
Taxonomy * Subject Heading
A multi-level vocabulary is essentially a way to group values into classes. A classification tells more about the values by placing them into well-thought-out categories.
Think of a classification as a tree - start with a trunk, and follow the trunk to a limb, then follow the limb to a branch, then follow the branch to a leaf. If you look at an individual leaf on the tree, you can back-track to the branch, which will lead you to the limb, which will eventually lead you to the trunk.
In a multi-level vocabulary, you can examine in which category a value belongs, and you can examine the relationships between categories as well. In some Multi-Level Vocabularies, the only connection between categories is a narrower-than / broader-than comparison (taxonomy). In others, you can compare like categories across broader categories (subject heading).
Relationship List
Thesaurus * Semantic Network * Ontology
Relational Vocabularies contain a mechanism to connect values. The relations are prescribed by various standards and protocols. There are a variety of relationships described for thesauri in the ANSI/NISO Z39.19 - 2003 standard, including broader than, narrower than, used for, and related value. In a relationship list, there are critical connections that are made in a standard way.
Think of a relationship list as seashells on the coast. You might find one on the San Diego coastline that looks exactly like one in Monterey Bay, except the San Diego shell has not been degraded by extreme waves. These two are probably related (similar to broader than). Or, perhaps you see a shell on the Oregon coast, and it looks similar to a shell in Woods Hole, Massachusetts. The two aren't exactly the same though, because they're different colors. There is still a relationship to be made (similar to related term). Perhaps you find a message in a bottle in Maryland. It's originally from Europe, and there's a seashell inside. In this case, you would want to relate the shell to other European shells (similar to used for).