If you make all of your scripts part of an addin, you can use syntax like this:
include("$ADDIN_HOME(com.cmpny.dept.myapp)\My Favorite Script.jsl");
You would define your addin with the alias com.cmpny.dept.myapp. Here's a sample addin.def file that defines it:
id=com.cmpny.dept.myapp
name="My great application"
host=Win
home="M:\mydept\myapp\Addin"
This addin is located in a fileshare mapped as the M drive.