Yes,  this is what string[] args is for in Program.cs.
The easiest way to ensure you have everything you need is to create your application from the Console Application template in Visual Studio.  
To do this:
- Go to File -> New Project...
- Select Console Applicationfrom the list of available templates
- Name your Solution
- Hit OK to finish creating the Project
This will ensure you have all the references needed and that the Program.cs class is setup properly.
Here is a psuedo example of what you can do in the Main method of your program in order to accept parameters at the command line:
static void Main(string[] args)
{
    if (args.Length <= 0) //Checking the Length helps avoid NullReferenceException at args[0]
    {
        //Default behavior of your program without parameters
    }
    else
    {
        if (args[0] == "/?")
        {
            //Show Help Manual
        }
        if (args[0] == "/d")
        {
            //Do something else
        }
        //etc
    }
}
Then at the command prompt the user can type:
yourProgamName.exe /?
yourProgramName.exe /d
As mentioned in an answer that was removed, there is a great library for handling complex Command Line options Here:
NDesk Options