Anthony, based on the volume of issues and the interest in a stable release of the module, I believe it is moderately popular. One of the things that might be holding it back, is the lack of a D7 stable release. However, that is getting resolved and a stable release is planned.
It has a good community that supports the back-end library (http://htmlpurifier.org/phorum/). As one of its maintainers, I believe it is a really good tool to clean-up and provide high quality HTML. As a current CISSP, I am excited about its very secure, default settings. It also has advanced abilities to provide full control over a filter, down to the regex of an attribute on each HTML tag.
I am going thru the recommendations of the seo checklist module. Was wondering how high on the popularity scale the html purifier module is in general terms. Thanks