@Paul I organize my scripts by business process. Real example:

FileCabinet/
  SuiteScripts/
    lib/ <- general utility libraries go here
      lodash.js
      moment.js
    sponsorship/ <- sponsor automation project
      sponsor-sc-overdue.js
      sponsor-wa-associateevent.js
      sponsor-wa-createinvoice.js
      sponsor-cl-generateevents.js
    rsvp-prevent-dup/ <- prevent duplicate Event RSVP project
      rsvp-prevent-dup.js
      rsvp-cl-validation.js
      rsvp-wa-prevent-dup.js