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

Expanding on the "By topic, then type" idea, here is what we've done on a larger recent project, and it worked out pretty well.
/Comments/Controllers/CommentsController.php/Events/NewCommentEvent.phpComment.php/Posts/Controllers/PostsController.php/Events/NewPostEvent.php/Post.php/Users/Controllers/UsersController.php/Events/UserLoggedInEvent.php/UserSubscribedEvent.php/User.php