Difference between NSWindowController Vs NSViewController
With iPhone SDK and Leopard SDK, they introduced view controllers, or NSViewController and UIViewController. As their names suggest what they do is to manage views
The view controllers are for managing views. Current trend in UI design is Single Window, Multiple View. What it means is that there is one Window and inside of it, different group of views designed for different purpose can be swapped in and out. So, the View Controllers handles these for programmers for well-established pattern. Currently view controllers are very important for iPhone and iPod touch programming, because the platform is based on Single-Window and Multiple View model. However, it doesn’t seem to me that using view controller is very popular for Mac. how about the window controller like NSWindowController? Its counterpart, UIWindowController doesn’t exist for the iPhone and iPod touch environment, because there is only one window for those environment. Unlike view controllers, the NSWindowController is for document based programs. Well, document based program can use multiple window. So, it is reasonable to think that NSWindowController is for document based programs as Apple’s document says.
I also come from iOS and started coding Mac apps a while ago, learning mostly from Apple's documentation.
My impression is that on the desktop, you almost never need NSViewControllers (one big exception would be a window with tabs and multiple views, like the GarageBand welcome screen).
Most of the time you have one NSWindowController per window. Learn first the relation between NSWindow and NSWindowController (and NSDocument, if you are making a document-based app).
Once you got that right, start experimenting with NSViewController.
UPDATE: It seems that since the introduction of storyboards for mac apps too, Apple expects that most of the view presentation logic should be migrated from the older NSWindowController to the newer NSViewController, more in line with how an iOS app is structured. I am not very knowledgeable on exactly where to draw the line, or what kind of code should remain in the window controller (or whether it still needs to be subclassed at all).
A Window Controller creates a traditional window and has all the traditional APIs.
A View Controller can also be shown outside of another view. It then gets a window frame but does not support the full traditional Window Controller API.
In addition to custom, modal, and show, a View Controller can also be presented in the modes sheet and popover.
So, View Controller has more presentation options and a more streamlined API but probably a few limitations in cases that are covered by the traditional Window Controller.