<SharePoint:CssRegistration
    runat="server"
    Name="/_layouts/styles/company/custom.css" />
<SharePoint:ScriptLink
    runat="server"
    Name="/_layouts/scripts/company/custom.js"
    Localizable="false" />

<SharePoint:CssRegistration
    runat="server"
    Name="/_layouts/styles/company/custom.css"
    id="customCss" />
<SharePoint:ScriptLink
    runat="server"
    Name="/_layouts/scripts/company/custom.js"
    Localizable="false"
    id="customJs" />

private static readonly long g_AssemblyTimeStamp = File.GetCreationTime(System.Reflection.Assembly.GetExecutingAssembly().Location).Ticks;
    protected override void OnInit(EventArgs e)
    {
        customJs.Name += "?rev=" + g_AssemblyTimeStamp;
        customCss.Name += "?rev=" + g_AssemblyTimeStamp;
    }

protected override void OnInit(EventArgs e)
{
        CssRegistration cssRegistration1 = new CssRegistration();
        cssRegistration1.After = "corev4.css";
        cssRegistration1.ConditionalExpression = "IE 7";
        cssRegistration1.Name = SPUtility.MakeBrowserCacheSafeLayoutsUrl("MyCustom CSS path _layouts folder", false);
        Controls.Add(cssRegistration1);
        base.OnInit(e);
}

<link rel="stylesheet" type="text/css" href="<%=SPUtility.MakeBrowserCacheSafeLayoutsUrl('custom css relative path', false)%>" />

<SharePoint:ScriptLink
    runat="server"
    Name="scripts/company/custom.js"
    Localizable="false"
    id="customJs" />

<script src="/_Layouts/scripts/company/custom.js?rev=HVORLc5FI20n7W90mjha3A%3D%3D"></script>

<link id="CssRegistration2" rel="stylesheet" type="text/css" href="/_Layouts/1033/styles/../../scripts/company/custom.css?rev=p63%2BuzTeSJc22nVGNZ5zwg%3D%3D"/>