I don't really understand the question. Is perl generating the page the javascript is on? In that case the number variable should be filled in as long as you put the content you are generating in a double quoted string(and assuming you assign a value to $number before you try to use it). But you show the javascript as a separate block. If you do something like the following, your $number should be replaced successfully.
$number = 7;
print << "END_OF_HTML";
<html>
<head>
<script type="text/javascript">
/* ... a bunch of JS .. */
messages[0] = new Array('upload/$number.gif','$number.gif',"#FFFFFF");
messages[1] = new Array('upload/$number.jpg','$number.jpg',"#DDECFF");
messages[2] = new Array('/upload/test.gif','Test description','black',
+'white');
/* ... a bunch of JS .. */
</script>
</head>
<!-- HTML body stuff -->
</html>
END_OF_HTML
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