How to programmatically launch an OS X app in minimized mode?

Uncheck visible at launch in your xib for main application window.

Implement - (BOOL)applicationShouldHandleReopen:(NSApplication *)theApplication hasVisibleWindows:(BOOL)flag in your app delegate class.

- (BOOL)applicationShouldHandleReopen:(NSApplication *)theApplication hasVisibleWindows:(BOOL)flag
{
    if (!flag) {
        [window makeKeyAndOrderFront:self];
        return YES;
    }
    return NO;
}