This is a problem which has been bugging me for a while now. I'm still pretty new with some of these patterns so you'll have to forgive me (and correct me) if I use any of the terms incorrectly.
My Methodology
I've created a game engine. All of the objects in my game engine use inversion of control to get dependencies. These dependencies all implement protocols and are never accessed directly in the project, other than during the bootstrapping phase. In order to get these objects, I have the concept of a service locator. The service locator's job is to locate an object which conforms to a specific protocol and return it. It's a lot like a factory, but it should handle the dependencies as well.
In order to provide the services to the service locator, I have what I call service specifiers. The service locator knows about all of the service specifiers in the project, and when an object is requested, attempts to get an instance of an object conforming to the provided protocol from each of them. This object is then returned to the caller. What's cool about this set up is the service specifier also knows about a service locator, so if it has any dependencies, it just asks the service locator for those specific dependencies.
To give an example, I have an object called HighScoreManager. HighScoreManager implements the PHighScoreManager protocol. At any time if an instance of PHighScoreManager is required, it can be retrieved by calling:
id<PHighScoreManager> highScoreManager = [ServiceLocator resolve: @protocol(PHighScoreManager)];
Thus, inversion of control. However, most of the time it isn't even necessary to do this, because most classes are located in a service specifier, if one required PHighScoreManager as a dependency, then it is retrieved through the service locator. Thus, I have a nice flat approach to inversion of control.
My Problem