The winmail.dat filter catches messages when they pass through its server-level rule, when they are received or sent by the CGP server. The filter analyzes the message and, if a winmail.dat attachment is found, that file is opened. If useful information (other files, images, RTF body, etc) is found, that information is extracted and the original attachment is discarded, replaced by the previously embedded data.
With default options, if nothing interesting is found in the winmail.dat file, no action is performed, and the message goes through unmodified.
As winmail.dat attachments are often specified as a subpart of a multipart/alternative MIME section, this can cause problems with iPhone, which, for unknown reasons, always choose to try to display the LAST subpart of a multipart/alternative section, even if it isn't able to do so. Most desktop software chose to display the "best" part, but only if they are able to.
To avoid this, you can also configure the filter to be more aggressive, using the --always-remove-winmail and --ignore-rtf-body flags on the command line. Even if nothing interesting is found in the winmail.dat attachment, the filter will still remove it, and will ignore any RTF body in there, using only the text and html parts already specified in the message.
Also, MS Outlook with older MAPI connector is known to convert messages on-the-fly into winmail.dat when they are open. The filter can't do anything about it, as it filters only message when they are received or sent, A fix has been issued by CGP. Make sure you have the latest CGP and MAPI connector versions installed.
Well, really, there is no way to prevent Outlook from sending winmail.dat files completely. However, you can reduce the number of such files it sends.
First, make sure you have the latest CGP server and MAPI connector installed.
Then, configure Outlook to send as HTML instead of as Rich Text, in Tools / Options / Mail format. If the MAPI plugin is used, you can also modify another setting: Account settings / Communigate pro, "Modify the settings", and in Troubleshooting tab select "Always convert RTF to HTML".
This, hopefully, should help. The winmail.dat filter will then be used to convert the remaining offenders, and those sent by external users.