The method you want to use is called ClientScript.RegisterStartupScript()

Here is some code I used a long time ago to register jQuery in a skin.

<script runat="server">
private void Page_Load(System.Object sender, System.EventArgs e)
{
    Page.ClientScript.RegisterClientScriptInclude("jquery", "http://ajax.googleapis.com/ajax/libs/jquery/1.2.6/jquery.min.js");
    Page.ClientScript.RegisterStartupScript(this.GetType(), "jQueryNoConflict", "jQuery.noConflict();", true);
}
</script>