Thanks for the push in the right direction. I kept trying different statements and here is what ended up working:
<?php if (is_home() and !is_paged()) { ?>
<script type="text/javascript">
new fadeshow(fadeimages, 920, 300, 0, 5500, 1)
</script>
<?php } ?>
Now the javascript thingy shows up on the home page but not page 2 or page 3 of posts. yay!
