Going from scratch, I prefer 2 different organizational styles.

Frontend (React.js)

• app
  • node_modules
  • client
    • main.js
    • main.css
    • components
      • FButton.js
      • FButton.css
      • SValidatedInputText.js {import ../utils/MyLeftPad.js}
      • SValidatedInputText.css
    • containers
      • HNav.js {import ./HNav.js}
      • HNav.css
      • DNavItems.js {import ../components/FButton.js)}
      • DNavItems.css
    • utils
      • MyLeftPad.js
      • MyLeftPad.css

• F - Stateless Functional component
• S - Stateful component (trying to avoid them as much as possible)
• H - Higher Order Container/Component
• D - Dump Container/Component

Backend (Node.js)

• node_modules
• app
  • client (if serverside rendering)
  • server
    • main.js
    • api
    • utils

Otherwise, I keep the existing structure given by scaffolds and starter projects like mern.io/

I was using an MVC style structure for one of my sites, but have recently changed to a module style structure.

For me, the change was for pushing to production reasons. In an MVC style, you could push individual files from different folders to production, but with a module style - I know what ever is in that folder, belongs to that module - so I just need to push that folder and be done. No concern about pushing an incorrect file or overwriting something that shouldn't be.

Neither is right or wrong I don't think - whatever works best for the project at hand.