I was able to test the POP3 integration against Gmail using the HtmlAgilityPack 1.4.6 referenced in the WAP project (so this version was pulled into the project while debugging) and was able to download and process over 400 spam messages (some failed due to the fact they had no subject).
So it would seem that having the HtmlAgilityPack 1.4.6 version in the WAP project might not be a bad idea, however I did not test if the AjaxControlToolkit was affected by this.
So it would seem that having the HtmlAgilityPack 1.4.6 version in the WAP project might not be a bad idea, however I did not test if the AjaxControlToolkit was affected by this.