I've added a custom tag of @modifies in the build section of the properties as follows:
-tag modifies:a:"This method modifies: "
This only shows up when I click 'generate javadoc' not when I am looking at the method in netbeans where I get the window that shows me all of the parameters the method takes and the other javadoc stuff.
EDIT: To be clear, this is not annotation related. Annotations are outside of the javadoc comment and are used at runtime and compile time, tags are only used by the javadoc generator.
We ended up wrapping our javadoc tags in html/bold so that it looked similar to the existing javadoc comments. It came out close enough that they looked the same.