Not a whole lot of difference. Intel boards generally run at 1333, while amd boards can post at 1600 on some of the newer boards. It's a tossup. I recommend 2x8 gb if you can find a kit for around $60; frys had some patriot in this format the other day.
The DDR3 standard changed about a year ago. So hardware produced since last year can AUTO default to DDR3-1600 CL11, both Intel and AMD. G.Skill DDR3-1600 kits are CL9 or lower, so you will still need to configure settings in BIOS/EFI. DDR3-1333 CL9 or lower is completely plug and play memory.
If you want performance, get DDR3-1600.
If you want plug and play, no BIOS adjustment at all, get DDR3-1333 CL9.