as siva says, bottom of the page is the 'ideal'. however, as for seperate files. this is only going to be practical as long as you don't reference asp.net elements from the page - ie:
<asp:Content ContentPlaceHolderID="jsCode" ID="jsCode1" runat="server">
<script type="text/javascript">
$(document).ready(function() {
getPoundsData();
});
function getPoundsData() {
var id = $("#ID").val();
var URL = '<%=Url.Action("GetPounds", "FundShareholder")%>';
var params = { id: id };
if (id != null)
SendAjaxCache("#" + $("#ShareholderID option:selected").text() + " RSP#", URL, params, null, ListDataShareholderPounds);
}
function ListDataShareholderPounds(data) {
if (data.length != 0) {
$('#shareholderPounds').html("");
$('#shareholderPounds').show();
$('#shareholderPounds').html(data);
}
};
</script>
</asp:Content>
notice the:
var URL = '<%=Url.Action("GetPounds", "FundShareholder")%>';
part in the js. what 'we' do is to add a content section to the master page at the very bottom to hold our js stuff. however, this only works inside the ViewPage (aspx) object. the ascx pages are 'ignorant' of any master page content sections.
We are currently working on systemizing the process whereby we save 'partial' js files with asp.net references inside them and then inject them into the page-flow via a filterattribute. we're at an early stage with this but the nice thing about this approach is that the partial js is treated as a file and is therefore cached for future visits to that page.
anyway, that's our current approach, would be interested to discover if peeps are using any similar mechanisms to inject js that contains asp.net object references.
cheers...
[edit] - here's a heads up on the approach i'm talking about (this wasn't our original inspiration, but is quite similar, tho is webforms, rather than mvc) - http://www.west-wind.com/WebLog/posts/252178.aspx or this one which IS mvc: http://poundingcode.blogspot.com/2009/12/injecting-javasript-into-aspnetmvc-with.html.
Finally found the article that inspired our 'search' in this: http://stackoverflow.com/questions/2957517/asp-net-mvc-routing-and-paths-is-js-files plus http://codepaste.net/p2s3po