Auto ISO on the Canon DSLR vs Automatic ISO on Nikon Digital SLR Cameras – Ken Rockwell:
Canon's Auto ISO, while not adjustable, is much smarter than Nikon's because it automatically shifts itself based on your zoom setting. It doesn't know if you have IS on or off.
Canon's Auto ISO is optimized to choose lower, cleaner ISOs in exchange for the slowest shutter speed you can hold safely – if your subject holds still, too. If shooting people, kids or action, it will usually result in shutter speeds that are too slow in dim light.
For most people, this Canon Auto ISO system is superior because it's easier to use. For myself and the minority of you who learn Nikon's more complex system, Nikon's system is superior for people and action photos because the lowest desired shutter speed can be set to 1/125 (or anything else), and the Nikons will then use higher Auto ISOs than Canon to try to maintain 1/125 in lower light so people don't get smeared. Canon's Auto ISO will be perfectly happy shooting indoors at 1/30 at wider angles, and your non-flash people photos will be blurred.