Do you know it's supposed to be executed from a command prompt?[You are not allowed to view links]
From there, you need to change its focus to the directory containing the GoodTool: chdir C:\Roms\GoodNGPx\
Then you should be able to run the tool using the commands it lists. For example: goodngpx.exe rename
If any errors come up, you will be able to make note of it instead of the window closing immediately as it does when run outside an existing console.