Generally, MVC frameeworks have a structure that looks something like:
/models
/views
/controllers
/utils
However, in a web application sui
If your apps share data, it could make sense (to me) to group the models together.
However, for the views and controllers it probably makes more sense to keep them separate, since I'm assuming they have separate business logic and presentations.
Further, if your apps are kept separately in version control (you are using version control, right? :), that makes the first or third option difficult to implement.
So all things considered, I'd probably separate the apps at the top level, as in your second example.