This seems to be a popular question - so figured I'd add my answer to the Wiki.

Every directory or file that you want to pass through must be clearly defined in two places:

1) webgui.conf

You must add it into the list in your webgui.conf like so:
  "passthruUrls" : [  "/images" ],

2) your apache site config

Inside your <VirtualHost> section you will need

        <Location /images>
          SetHandler None
        </Location>

You then create your "images" site folder at

"/data/domains/[mydomain]/public/images"

You will need to restart WebGUI once you've done this.

If you also want to have the ability to run non-WebGUI CGI scripts, this can be accomplished by adding the folowing

<Directory "/data/domains/[mydomain]/public/[sitefolder]/cgi">
   Options +ExecCGI
   AddHandler cgi-script .cgi .pl
</Directory>

This assumes that your CGI parent [sitefolder] has been defined as specified above.  Again, you will need to restart WebGUI after making this change.