Is uploading/download executable files harmful in drupal? In my site design, I have a field that is designed to hold an executable file (.exe, .bat, etc), for users to upload and download. I took pause as I was typing these extensions into the Allowed file extensions setting on the file field. Is this ok? What do I need to be aware of?
You'll want to make sure that your server is not configured to execute files of the given extensions in any way.

As a general precaution, you might also configure that file field to use the Private file system, which allows access to those files to be controlled by Drupal's permissioning system.