By type
/Controllers
/Events
/Models
By topic
/Comments
/Posts
/Users
By topic, then type
/Comments
/Controllers
/Events
/Models
/Posts
/Controllers
/Events
/Models
/Users
/Controllers
/Events
/Models
Mixed
/Comments
/Controllers
/Events
/Models
/Posts
/Users
It depends on the project for me, if it has a large enough scope then I would usually do something quite similar to @frankdejonge but if I was building a small microservice for example I would tend to go by type.