I have implemented the ability to upload, download, delete, etc. using the FtpWebRequest class in C#.  That is fairly straight forward.
What I need to do now is support sending arbitrary FTP commands such as
quote SITE LRECL=132 RECFM=FB
or 
quote SYST
Here's an example configuration straight from our app.config:
<!-- The following commands will be executed before any uploads occur -->
<extraCommands>
     <command>quote SITE LRECL=132 RECFM=FB</command>
</extraCommands>
I'm still researching how to do this using FtpWebRequest.   I'll probably try WebClient class next.  Anyone can point me in the right direction quicker?  Thanks!
UPDATE:
I've come to that same conclusion, as of .NET Framework 3.5 FtpWebRequest doesn't support anything except what's in WebRequestMethods.Ftp.*.  I'll try a third party app recommended by some of the other posts.  Thanks for the help! 
Syntax FTP [-options] [-s:filename] [-w:buffer] [host] key -s:filename Run a text file containing FTP commands. host Host name or IP address of the remote host. -g Disable filename wildcards.
I don't think it can be done with FtpWebRequest... The only way to specify a FTP command is through the Method property, and the documentation states :
Note that the strings defined in the
WebRequestMethods.Ftpclass are the only supported options for theMethodproperty. Setting theMethodproperty to any other value will result in anArgumentExceptionexception.
SITE and SYST are not among the predefined options, so I guess you're stuck...
Don't waste time to try the WebClient class, it will give you even less flexibility than FtpWebRequest.
However, there are plenty of third-party FTP implementation, open source or commercial, and I'm pretty sure some of them can handle custom commands...
The FtpWebRequest won't help you as Thomas Levesque has said in his answer. You can use some third party solutions or the following, simplified TcpClient based code which I have refactored from an answer written in Visual Basic:
public static void SendFtpCommand()
{
    var serverName = "[FTP_SERVER_NAME]";
    var port = 21;
    var userName = "[FTP_USER_NAME]";
    var password = "[FTP_PASSWORD]"
    var command = "SITE CHMOD 755 [FTP_FILE_PATH]";
    var tcpClient = new TcpClient();
    try
    {
        tcpClient.Connect(serverName, port);
        Flush(tcpClient);
        var response = TransmitCommand(tcpClient, "user " + userName);
        if (response.IndexOf("331", StringComparison.OrdinalIgnoreCase) < 0)
            throw new Exception(string.Format("Error \"{0}\" while sending user name \"{1}\".", response, userName));
        response = TransmitCommand(tcpClient, "pass " + password);
        if (response.IndexOf("230", StringComparison.OrdinalIgnoreCase) < 0)
            throw new Exception(string.Format("Error \"{0}\" while sending password.", response));
        response = TransmitCommand(tcpClient, command);
        if (response.IndexOf("200", StringComparison.OrdinalIgnoreCase) < 0)
            throw new Exception(string.Format("Error \"{0}\" while sending command \"{1}\".", response, command));
    }
    finally
    {
        if (tcpClient.Connected)
            tcpClient.Close();
    }
}
private static string TransmitCommand(TcpClient tcpClient, string cmd)
{
    var networkStream = tcpClient.GetStream();
    if (!networkStream.CanWrite || !networkStream.CanRead)
        return string.Empty;
    var sendBytes = Encoding.ASCII.GetBytes(cmd + "\r\n");
    networkStream.Write(sendBytes, 0, sendBytes.Length);
    var streamReader = new StreamReader(networkStream);
    return streamReader.ReadLine();
}
private static string Flush(TcpClient tcpClient)
{
    try
    {
        var networkStream = tcpClient.GetStream();
        if (!networkStream.CanWrite || !networkStream.CanRead)
            return string.Empty;
        var receiveBytes = new byte[tcpClient.ReceiveBufferSize];
        networkStream.ReadTimeout = 10000;
        networkStream.Read(receiveBytes, 0, tcpClient.ReceiveBufferSize);
        return Encoding.ASCII.GetString(receiveBytes);
    }
    catch
    {
        // Ignore all irrelevant exceptions
    }
    return string.Empty;
}
You can expect the following flow while getting through the FTP:
220 (vsFTPd 2.2.2)
user [FTP_USER_NAME]
331 Please specify the password.
pass [FTP_PASSWORD]
230 Login successful.
SITE CHMOD 755 [FTP_FILE_PATH]
200 SITE CHMOD command ok.
                        You can try our Rebex FTP component:
// create client and connect 
Ftp client = new Ftp();
client.Connect("ftp.example.org");
client.Login("username", "password");
// send SITE command
// note that QUOTE and SITE are ommited. QUOTE is command line ftp syntax only.
client.Site("LRECL=132 RECFM=FB");
// send SYST command
client.SendCommand("SYST");
FtpResponse response = client.ReadResponse();
if (response.Group != 2) 
  ; // handle error 
// disconnect 
client.Disconnect();
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