I found the answer to this, from John Mitchell's Blog. Simply place the following code after the register tags in your skin file. It will add the script reference to the HEAD tag.

<script runat="server">
Private Sub Page_Init(ByVal sender As System.Object, ByVal e As System.EventArgs) Handles MyBase.Init
'add a script reference for Javascript to the head section
Dim oLink As New HtmlGenericControl("script")
oLink.Attributes("language") = "javascript"
oLink.Attributes("type") = "text/javascript"
oLink.Attributes("src") = SkinPath & "MyJavascript.js"
Dim oCSS As Control = Me.Page.FindControl("CSS")
If Not oCSS is Nothing Then
oCSS.Controls.AddAt(0, oLink)
End if
End Sub
</script>