As far as I can tell the only type of files the PTO will accept is ADCII compatible files. I'm pretty sure that means text, and text only.
I have a book that talks about submitting machine code, but I don't know how that would work with the ASCII requirement.
In addition to the CD, you also get to submit the actual patent (which is on paper), so you can include any type of image (or whatever else) that you want, so long as it is actually printed out.
The whole thing seems pretty arcane to me, but I don't really understand it very well yet either.