A quote from _The Art of Shaolin Kung Fu_ (The Secrets of Kung Fu for Self-Defence, Health, and Enlightenment) by Wong Kiew Kit: "Southern Shaolin Kung Fu is characterized by solid stances, powerful arms and elaborate hand techniques, in contrast with the elegant jumping, extensive movements and wide range of kicking attacks of the Northern Shaolin version." _Taijiquan, Classical Yang Style_ by Dr. Yang, Jwing-Ming contains a short section on northern and southern styles in its general introduction. He gives some reasoning as to why differences developed in the section, but there's too much to quote the whole thing, so I'll just quote the conclusions here (which are still a bit).
1. Northern Chinese are generally taller, and therefore prefer long or middle range fighting, while southern Chinese are shorter, so middle and short range fighting are emphasized.
2. Northern styles emphasize more kicking techniques for long range fighting, while southern stylists specialize in more hand techniques and a limited number of low kicks. This is why it is commonly said: "southern fist and northern leg" in Chinese martial arts society.
3. Southern stylists focus on training a firm root, while northern stylists like to move and jump around. Moreover, northern martial stylists have more expertise in horse riding, and martial techniques from horse back, while southern martial styles specialize more in fighting on boats and on the ground. [historic difference in transportation methods]
4. Because southern styles generally emphasize more hand techniques, grabbing techniques such as Qin Na have developed more.
So there's a little bit on the difference. The one major one I had heard was the emphasis of kicks in northern styles and hand techniques in sourthern styles. Someone with more knowledge can probably provide more and/or better information than this though.