If you really want to "get" the original MVC, see the classic book "Smalltalk, Objects, and Design" [1] which explains MVC and other OO architectures as well as the principles behind them, which might guide you to picking an appropriate structure for applications that don't fit the GUI/MVC paradigm.
[1] http://www.amazon.com/Smalltalk-Objects-Design-Chamond-Liu/d...
Looking back at it now, it had everything your typical web MVC framework has, just slightly diffrent:
* Models, with cleanly encapsulated functionality, but without an ORM. I only built small websites, so all related database tables were managed by the same model.
* Controllers that handled all input and delegate it to models.
* Views in the form of HTML code following the controller code in the same file, but strictly separated.
* "Forms" that abstracted away the controller/view and input validation of forms in a neat, reusable package.
My point is that whatever you come up with that actually works well and lets you be productive will more-or-less resemble MVC.