To do this, you would usually subclass NSWindowController and change the File's Owner class to your WindowController subclass in the nib.
EDIT:
If you aren't doing a document-based app, and just want an NSWindowController of your own to do on-demand loading of Nibs (completely reasonable), then you'd delete the window from your nib and instantiate an NSWindowController
subclass programmatically, using it explicitly to do your window loading...
@implementation MyApplicationDelegate {
MyWindowControllerSubclass *windowController;
}
-(void)applicationDidFinishLaunching:(NSNotification *)notification {
windowController = [[MyWindowControllerSubclass alloc] initWithWindowNibName:@"MyWindowNib"];
[windowController showWindow:nil];
[windowController.window makeKeyAndOrderFront:nil];
}