Where to put plain object classes?

* What if a class is only to be used statically. I.e., you NEVER instantiate this class for any reason because all of its methods are static.

It's been my experience that these include/require statements are the source of much code redundancy and many bugs.

Code redundancy and bugs? It's only one line of code. I can live with one redundant line!
I'm curious what kind of bugs you had with include/require you don't have with an autoloader.

* What if you must supply arguments to the constructor for the class? This would in all likelihood cause a fatal error if CodeIgniter tried to instantiate the object without providing these parameters.

You can pass arguments to the loader class in the second parameter:

$params (array) – Optional array of parameters to pass to the loaded library’s constructor

http://www.codeigniter.com/userguide3/li...-reference

* What if I need multiple instances of MyClass to perform some operation.

Then use require_once!

Maybe I'm too old school, but I don't understand why people have trouble doing simple things just because they use a framework. What would you do in plain PHP? If CI doesn't provide what you're trying to do then do it in plain PHP.