Do you know how to make an icon for a folder? If so, take the app off the dock, change the logo, and put it back on.
So the long version:
1. Make icon (in PS or something similar)
2. (If parts are transparent) Save as Tiff and preserve transparency
3. (if parts are transparent) Use Pic2Icon to clean it up a bit
4. Remove app from dock
5. ⌘i on the .tiff
6. Click on the small icon in the corner, ⌘c
7. Find the app, ⌘i, click on the small icon, ⌘v
8. Drag app to dock again
It really doesn't take very much time.