I'm using Cygwin/X to run linux programs remotely and it's real slow.
 

I am running programs remotely but they are terribly slow. I'm on a windows machine which may be my first problem. I have killer ping and download speed so they should run fine. What can I do to resolve this.

Welcome to LQ. Are you running these programs with a GUI or in a terminal/text box? Assuming your running them with a GUI, how are you achieving the connection? Remote GUI applications are usually a little slow, or at least slower, to begin with. My experience is that using Cygwin/X tends to be awfully slow. Instead a couple of options would be to look at FreeNX for remote desktop viewing (FreeNX incorporates SSH functionality and is a secure means to view the desktop), or XMING if you just want to launch an application, like XIRC or Gimp, for example and operate it on your Windows machine.

X is slow.

If you feel it is cygwin then might try mobaterm just to see.