Funciona igual con Flash:
Código HTML:
<script type="text/javascript">
function capa(op){
document.getElementById('Capa').style.display = (op==1)?'block':'none';
}
</script>
<a href="#" onclick="capa(1)">mostrar</a> <a href="#" onclick="capa(0)">ocultar</a>
<div id="Capa" style="border:solid #6699FF 1px;background:#FFFFE6; width:300px;">
<iframe src="http://www.albinoblacksheep.com/games/missilegame3d"></iframe>
</div>