If you're going to use it with anything moderately powerful, you'd be better off going Intel. If it's just a basic HTPC box, that opens things up a lot. I have some AMD E-350 ITX boards which are decent low power basic computers for either HTPC or basic office apps. If you have to have something newer, the new quad core J1900 based units are good and -very- low power (sub 10w).
For something more powerful, Intel gets the nod since they have such a broad set of CPUs to choose from from dual-core, dual-core hyperthreaded, full quad core, or full quad hyperthreaded. I've always had good luck with Gigabyte boards, and they have a B85 based ITX board, with integrated WIFI, HDMI, DVI, USB3/2, 2 DIMMS, and a full length PCIe slot for...