Under contract with LBNL, I have written an HDR capture program that works with the Canon EOS 5D camera under Mac OS X, and should work with other Canon EOS cameras as well. When open from the Finder, the application triggers a sequence of image captures, saving them to the laptop across a USB or Firewire connection. Setting the camera in manual mode, the sequence begins at the fastest available shutter speed and works its way down until it finds the first exposure with over-exposed pixels in its thumbnail. It saves this image along with the previous one, and continues downward in the exposure range (longer shutter times) for the number of stops and images you specify in a configuration file.
Unfortunately, CanonHDRcap does not work from the command line, as the Canon software requires building with CodeWarrior and an outdated Carbon application package model, which doesn't support command-line operation. However, using the OS X "open" command, you can run it from a batch file and determine when it finishes based on another output file it creates, specifying the names of the image files it has created. (My next task is to build a script that runs hdrgen automatically afterwards, which should be easy enough.)
I've put the app. on my website for any masochistic beta testers who want to have a go with their Canon EOS camera. It produces beautiful results, so long as you don't mind lugging a laptop and a tripod with you; it eliminates all camera movement and does a much better job capturing the full range than auto-bracket mode. The link is below:
Most of the camera settings are left as set on the camera, including aperture, white balance, JPEG/RAW mode, etc. The one thing I'm sure doesn't work is storing both JPEG and RAW images at the same time, but let me know if you run into any other problems.