The main difference is that for H55 chipset,if you use a Lynnfield CPU(Like i5 750,i7 860....) you can use CrossFire(if the board has 2 PCI-E slots), but if you use a Clarkdale CPU,then you can't use CrossFire(even if the board has 2 PCI-E slots),because with Clarkdale,you'll have an integrated VGA too.
^+1. Pretty much Core i3s & Core i5 600s have integrated graphics on them which can only be used if you pair it with a H55 chipset based motherboard. You can't CFX/SLI on any board using a Core i3/Core i5 600 chip. Also, H55 boards tend to be cheaper, intended for HTPCs and smaller computers of that sort.