I am not an expert on motherboards, but from my reading and limited experience, I think it is a matter of user preference. I have used Asus boards and not experienced any problems. Also it depends how you are planning on using your computer. You must match your board to your CPU.
Hope this helps.
Is it just me or does the original poster seem to have confused the motherboard and the CPU?
There are two main CPU manufacturers, AMD and Intel. To run the CPU you need a motherboard for it to go in, these are made by companies such as Asus, Gigabye, Asrock, MSI, Sapphire etc.
You need to make sure the motherboard you get is compatible with the CPU you get. Most manufacturers make boards for Intel CPUs and different boards for AMD CPUs. Telling which are which is easy, they will say Intel or AMD. The harder part is the socket and specific CPU compatibility.
For AMD if you want an Athlon II or a Phenom II (ie. their newer range of CPUs) you will want an "AM3" motherboard, which takes DDR3 memory.
For Intel they usually have a code with a number for the socket, which is how many pins it has. It's easiest to look at the CPU compatibility list for the motherboards.
As far as different motherboards for the same CPU go, it's purely down to features and size. As for picking between CPUs goes, AMD typically offer better bang for your buck, but Intel does offer faster processors if you have the money. Tomshardware has pages of benchmark charts for you to compare the performance.
Personally I'm an AMD person, with one ECS motherboard and an older Athlon x2 5000be and a just arrived Asus mini itx motherboard with a phenom II x6.