I have some include files (.inc) that have classes in them that are used by multiple modules. Where should these be stored so that they are accessible to files in a modules .info file? Preferably without having to store copies of the files in each modules directory.
Probably the sanest way to do this would be to create a new module which has little to no functionality, but includes the .inc files; then make your other modules dependent on that module. As you develop the other modules and find other functionality you want to share between them, just implement it in the "parent" module, and away you go.
If adding another module is objectionable for some reason, you could implement it as a "library" and use the Libraries API module - but that's intended for Drupal-external third-party PHP libraries like TinyMCE, not things you've built yourself.