Adding default command line options when opening a particular filetype

I would say that the easiest tool is Nirsoft FileTypesMan.

Launch it and find the extension you want to modify.

In the lower pane, find the action and modify it to either emacs.exe -fs %1 or emacs.exe %1 -fs

... Assuming Emacs.exe is the program name. Also, having never used it, I am not sure what order to provide the arguments. %1 is the file name, so use whichever one works.

Looking under the hood at what Nirsoft FileTypesMan does, you can do the same thing manually as follows:

1. Look in

   HKEY_CLASSES_ROOT\.ext
   

   at the (Default) value, for whatever file extension .ext you care about. Call that value {class_for_ext}.

2. Look in

   HKEY_CLASSES_ROOT\{class_for_ext}\shell\open\command
   

   at the (Default) value. That's the command line which Windows Explorer will run, and which FileTypesMan will let you edit.