If I have an Excel list of lat/long coordinates (which I can easily convert into X/Y image coordinates), what is a good way of placing points or drawing lines in an image using those coordinates? Obviously, I can do it manually, but I'm trying to construct a new process, and manual doesn't work for that.

I am not sure what programs might be best to use, probably something that has a scripting language. I can convert coords into script commands pretty easily. Then I would just run the script and it would draw the stuff onto the image, which I could bring into Photoshop or Fractal Terrains as an overlay.