Joshua Hutchinson wrote:

Well, the one problem I can see if that it becomes very hard to link to a specific file within the zip file.

Internet Archive already has a solution. They can extract a jpg from a zip on the fly. Look at this url: http://ia331340.us.archive.org/zipview.php?zip=/3/items/goodytwoshoes00newyiala/goodytwoshoes00newyiala_flippy.zip&file=0002.jpg "Borrowing" that code should be easy.

For instance, with the audio files, we have index files that let you link directly to a particular section/chapter. If that file is within a zip file, that becomes a problem.

No problem. Keep the index outside the zip file then.