To add border to Jmol applet:

in Jmol exstension in file Jmol.body.php to the function renderInternalJmolApplet add the following string after the statement containing "jmolSetAppletColor"

$output .= "jmolSetAppletCssClass(" . $sep . "jmol" . $sep . ");";

The MediaWiki:Common.css‎ should containe something like:

.jmol {

border:1px solid #a1a1a1;

}