StreamReader reader = new StreamReader("c:\\temp\\1.txt",Encoding.Default);
            string source = reader.ReadToEnd();
            Regex reg = new Regex(@"(?is)(?<=<JSContainer>).*?(?=</JSContainer>)");
            Match mm = reg.Match(source);
            source = reg.Replace(source, "<script src='/Assets/Scripts/js.axd?files=jquery.validate.js,jquery.validate-vsdoc.js' type='text/javascript' ></script>");

------解决方案--------------------
C# code
            string str = @"<JSContainer>
<script src=""Assets/Scripts/jquery.validate.js"" type=""text/javascript""></script>
<script src=""Assets/Scripts/jquery.validate-vsdoc.js"" type=""text/javascript""></script>
</JSContainer>";
            Regex reg = new Regex(@"(?is)<JSContainer>(?:\s*<script\ssrc="".*?/([^""/]+?)"".*?</script>)*\s*</JSContainer>");
            Match m = reg.Match(str);
            string result = "<JSContainer><script src='/Assets/Scripts/js.axd?files=";
            foreach (Capture c in m.Groups[1].Captures)
                result += c.Value + ",";
            result = result.TrimEnd(',') + "\" type=\"text/javascript\"></script>";
            Console.WriteLine(reg.Replace(str, result));