It's cut and dry.
If the motherboard uses DDR3 RAM it's the same RAM whether it's bundled with 3 sticks for Triple Channel or 2 sticks for dual channel. Different RAM may have slightly different voltages but should work in all motherboards.
Assuming you are building an x58 based system with something like the Core i7 920 you are using Triple Channel.
You will want to get RAM like this:
6GB DDR3 (3x2GB) 1066MHz
It's better to get 1066MHz with lower timings than to get 1600MHz with higher timings (it's complicated). More than 6GB is a complete waste unless you have some very unusual requirements. It's quite difficult even when doing considerable multitasking to notice a difference above 4GB but I still recommend 6GB above 3GB. If I had a high-speed SSD I might actually consider the 3GB, but I won't get into the relationship between hard drives/SSDs, multitasking and RAM. I've done EXTENSIVE testing and know a lot about computers.
There's really not much to think about. You buy your motherboard and it will specify the details though all DDR3 should fit in all motherboards.