I've got a Chrono Cross iso that does this:

Thanks to maggiekarp and BROJ at the Compendium for the clothing, hair, and skin redesign.

It's sitting on my hard drive. If others are to learn the joys of the Guile -> Magil (that's Magus as he existed in Radical Dreamers) hack, I need to be able to create a patch for a 600+MB iso file.

Is there any patching program out there that can handle files this big? It's not as simple as running the iso through Lunar IPS like we do with SNES games, is it?

You can use Ppf Studio to make the patch.

Is there a way to make a .PPF patch for an ISO ripped with CloneCD?

CloneCD uses the formats .ccd and .img, but all the programs I have looked at seem to only support .bin.

Yup IMG, ISO, and BIN are all exactly the same as long as you used the right settings.