The most common way I see on the wild is by separating in categories:

  - package.json
  - src
    |- main.js
    |- components
       |- pages
       \- widgets
    |- directives
    |- helpers
    |- mixins
    |- router
    \- store

This works for both small projects (but you might not have directives/mixins/router/store) and larger projects (but you might have to add more subfolders inside components/pages because you will start breaking down components).