The Auslogics duplicate file finder is good tool.
how do you know which is the right one to keep and which you should delete.
As Reza-Ameri commented, you don't just want to go around deleting applications that have gone through the installer. If you find the Kindle.exe or Sim3.exe (I don't know their actual names) in multiple folders and you can't remember why you put them there, you could run regedit and search the registry for that folder to see if the installer has referenced the folder..
You would have to decide based on folder location, date modified, and file contents, which files should be saved and which should be deleted.
Only you can make that determination.