What is the purpose of annotations in Java? I have this fuzzy idea of them as somewhere in between a comment and actual code. Do they affect the program at run time?
Annotations are primarily used by code that is inspecting other code. They are often used for modifying (i.e. decorating or wrapping) existing classes at run-time to change their behavior. Frameworks such as JUnit and Hibernate use annotations to minimize the amount of code you need to write yourself to use the frameworks.
Oracle has a good explanation of the concept and its meaning in Java on their site.