JavaDoc: where to add notes/remarks to documentation?

As far as I know, there isn't any dedicated Javadoc tag for notes or remarks. Generally, the first sentence of Javadoc should give a brief description of the class/method/field. Then the full description should follow. And if you want to include any notes, a specialized paragraph with a "Note:" prepended should suffice.

/**
 * Brief description. Full description of the method, generally without
 * implementation details.
 * <p>
 * Note: Additional information, e.g. your implementation notes or remarks.
 * </p>
 * @param input description of the parameter
 * @return description of return value
 * 
 * @since version
 * @author name of the author
 */
public boolean doSomething(String input)
{
    // your code
}

With iteration 8 of the Java programming language, developers finally have been provided with three additional tags they can use in their code's documentation – and which should meet your needs: @apiNote, @implSpec and @implNote (cf., for instance, for a more detailed discussion: blog.codefx.org/java/new-javadoc-tags/).