Is it possible to change the file name prefix that the camera uses? A firmware hack maybe. I know I can assign names using the Canon utility to download, but mostly when putting a few pics onto the computer I just read the card directly.
I don't think you can on the Rebel series. The 7D got the option to set the prefix with a firmware update this summer, and I think it's been in the higher end models for a while. And I may be mistaken but I don't think the Magic Lantern firmware hack addresses this.
But that's not the end of things. As part of my workflow, I use a script for reading files off of my memory cards which copies them to my computer, renames the files using jhead (you could also use ExifTool), and for good measure also copies them to off-site backup.
This gives me a lot more flexibility than the in-camera settings ever could. Even though my camera does allow changing the prefix, it doesn't let me embed the date or other useful information in the filename. Since you say you work by reading the card directly, it may be easy for you to adapt to a similar process.