First, I'm assuming the organization for ASP.NET Identity, so the answer does not turn up a textural wall.

Assuming the following scenario:

  

• Controller for user (UserController);
  
• ViewModel for user actions;
  
• Class representing the user entity;
  
• Class representing the user repository;
  
• Some User Views have images;
  
• Some User Views have specific scripts and css's.
  

How can I organize the above scenario?

In ASP.NET Identity this is already organized for you as follows:

• Controller for User: Controllers/AccountController ;
• ViewModels for User Actions: Models/AccountViewModel ;
• Class representing the User entity: ApplicationUser , in Models/IdentityModels . This does not mean that additional entities should be in the IdentityModels source. It is best to leave one font per class;
• Class representing the User repository: If you are using the Entity Framework, the Entity Framework is the repository not only of User, but of all system entities . In an ASP.NET MVC5 application, it is within ApplicationDbContext ( Models/IdentityModels ), derived from IdentityDbContext , which contains IDbSet<TUser> Users . This Users is the repository;
• Some user views have images: You can save the user's images to the database in the Content/Images directory or use Gravatar .
• Some User Views have specific scripts and CSS: You would have to mount @section s dynamically. Usually the project is configured with two: scripts and views . See your _Layout.cshtml file to see where those sections will be written. It's not worth putting this here. This part deserves a separate question.

Where should I write the code for all ViewModels? Should these be in the same location as the user entity?

In a directory ViewModels , separated from other directories ( Models , Controller , Views , ...).

And the images of a specific View should be grouped in the Content folder?

Yes. I usually use Content\Images\MinhaView\ . You can create as many subdirectories as you want from there. Just do not forget to set a index.html file for each level, to avoid problems with the publication (if the directories are empty, Web Deploy does not create the directories at the destination of the publication).