ENDNOTE is a fine program. It allows the author to enter references in a central registry, or to get them from the Internet, for eventual insertion into a document, and the program automatically applies APA style to the references and citations. WORD 2007 has introduced a similar feature.
Citation Checker operates quite differently. It works on already written documents, parsing them to see that every citation is in the reference list and every reference is cited. It caters to the writing style that I use, namely, I madly write the document, putting in parentheses where a citation should go so that I do not interrupt the flow while I am being creative. As I revise, either on my own initiative or in response to an editor's suggestions, citations have to be added or dropped when the text changes. That's usually when the rot sets in.
In a sense, then, Citation Checker complements the competition. In fact, my very organized wife uses ENDNOTE to write her scientific papers. Before submitting, she always reviews the manuscript with Citation Checker, and invariably it finds things to complain about.
For editors and reviewers, who are working with what is supposed to be a finished product, Citation Checker is an indispensable tool.