Intenta con esto, me dices como te va ...
Código:
<script language="JavaScript"><!--
images = new Array(4);
images[0] = "<a href = 'index.htm'><img src='banners/banner.gif'></a>";
images[1] = "<a href = 'index2.htm'><img src='banners/banner2.gif'></a>";
images[2] = "<a href = 'index3.htm'><img src='banners/banner3.gif'></a>";
images[3] = "<a href = 'index4.htm'><img src='banners/banner4.gif'></a>";
index = Math.floor(Math.random() * images.length);
document.write(images[index]);
</script>