The main difference between these are form-factor and power connectors.
The uATX form factor, also know as Micro-ATX, is useful if you are looking to build a smaller cased system.
Currently, there are 3 form factors that are common. Here's the breakdown with all sizes in inches.
Standard ATX = 12 x 9.6
uATX/Micro-ATX = 9.6 x 9.6
Mini-ITX = 6.7 x 6.7
With a few exceptions, motherboards and cases are compatible if it fits, so a full size case can usually handle all three sizes of mobo.
So the ASUS H87M-E will fit in more cases while the Gigabyte GA-H87-HD3 fits in fewer cases, but has more expansion slots.
Aside from that, the two are very comperable