In these cases I usually add a ContentPlaceHolder in the tag of my Master Page.
Alternately I've used a method (usually in a utility class or PageBase class) that puts the script string in a List and stores it in the ASP.Net Context like so:
List<string> javaScriptUrls = new List<string>();
url = url.ToLower();
javaScriptUrls = Context.Items[JS_KEY] as List<string>;
if (javaScriptUrls == null)
{
javaScriptUrls = new List<string>();
javaScriptUrls.Add(url);
}
else
{
if (!javaScriptUrls.Contains(url))
javaScriptUrls.Add(url);
}
Context.Items[JS_KEY] = javaScriptUrls;
Then OnPreRender of the MasterPage, it reads this List from the Context and builds tags in the header.
List<string> _javaScript = Context.Items[JS_KEY] as List<string>;
foreach (string js in _javaScript)
{
HtmlGenericControl script = new HtmlGenericControl();
script.TagName = "script";
script.Attributes.Add("type", "text/javascript");
if (js.StartsWith("~/"))
script.Attributes.Add("src", head.ResolveUrl(js));
else
script.Attributes.Add("src", js);
head.Controls.Add(script);
AddHeaderLineBreak(head);
}