Well personally, my favourite has always been FTP 🙂
This is by far the easiest way to do it. You dont say though how you want to go about it. If you want a web front end, then uploading a script is the same as uploading any other filetype (with the exception that you can get away with different enctypes in the HTML form).
If you give a bit more information, then we can probably give you a bit more help 🙂