Sheldon explains it better than I could...
http://sheldonbrown.com/rim-brakes.html
But, I believe the short answer is: longer pads for more surface area to increase braking in dirt/mud conditions.
These are the kind of pads that are on my commuter, which has old timey single pivot brakes:
http://www.amazon.com/Kool-Stop-Bicycle-V-Type-Compound/dp/B001T35RSC/ref=pd_bxgy_sg_img_y
I got the replacement pads for these by accident:
http://www.amazon.com/Kool-Stop-Bicycle-Dura-Ace-Ultegra/dp/B0014BRW6E/ref=pd_bxgy_sg_img_y
The latter is shorter than the former, but other than that, what's the difference?
I think I've seen the shorter style more on road bikes, which I think still have dual-pivot brakes right?
I've seen the longer style more on XC bikes like my fSO's, which have cantilever brakes
Is there any difference in performance?
Why is one used over the other?
Sheldon explains it better than I could...
http://sheldonbrown.com/rim-brakes.html
But, I believe the short answer is: longer pads for more surface area to increase braking in dirt/mud conditions.
I am sure Sheldon Brown has a good explanation. That said, don't worry about it. If they fit you can use either. I've switched between them on 'cross bikes and felt no difference what so ever. Most 'cross bikes have gone to the shorter road style simply to have more compatibility with road stuff since the MTB brake pad market is largely disc at this point.
Anyways, assuming they fit, keep what you have.
FWIW, I don't think Sheldon has an explanation as to why one is longer than the other, but if it's about the same, I won't worry about it