Hi Michael, yes i'm referring to the automate/photomerge function in CS3 which in comparison to the same feature in CS2 is a major improvement from my experience - I had also read this in a review so I was eager to try it. CS3 seems to be able to match images with different exposures and different saturation levels (typical of my frantic photography when a supercell is looming!), correct these differences and stitch them fairly well - CS2 simply couldnt do it. The most impressive thing is that it will merge wide angle shots (mine were taken with Canon 17-40L and 10-22 lenses) and then allows you to 'correct' the edge distortion remaining on the sides of your new panoramic image - its brilliant. I'll put some more examples up when I can.
Richary, obviously im not sure which Canon software you have but the Canon photostitch I have used in the past wasnt bad but had its limitations. There was little forgiveness if you didnt line up the shots well, get the exposures right for each shot and didnt cope well with merging wide angle shots. I was left with obvious stitch lines which werent good. If you get a chance, try both and compare and let us know what you think.