In your master page you can add a content area within the <head> block. We call ours "HeadContent".
Our master page's head block looks like this:
<head>
...
<asp:ContentPlaceHolder ID="HeadContent" runat="server" />
</head>
From your content pages you can then include custom scripts/css etc:
<asp:Content runat="server" ID="Head" ContentPlaceHolderID="HeadContent">
<script type="text/javascript" src="<%= Url.Content("~/scripts/gradebook.js") %>"></script>
<style type="text/css">
@import url('<%= Url.Content("~/styles/gradebook.css") %>');
</style>
</asp:Content>