I usually tend to go with whatever boards are recommended in the threads by Renethx or Assassin for HTPC builds. However, I've used boards from Asus, ASRock, Biostar, MSI, ECS, A-Bit, Gigabyte, Intel, and some off-brand boards as well. I've never been into overclocking or tweaking the boards for extra performance, mainly because I don't have a need to squeeze every last bit of speed out of them for what I use them for. All of my HTPC builds have used Asus, ASRock, Intel, or MSI motherboards. The only bad boards I've ever owned that required warranty replacements were from Intel, and I had two bad boards in a row of different models. Needless to say I'm not going to waste my time on another Intel board. Motherboards these days from any (almost) name vendor will work in a HTPC. The main thing to consider is what features they offer in the way of expansion (i.e., number of PCI-e/PCI slots, SATA 2/3 ports, USB 2/3 ports, etc.). Depending on your planned setup, you may not even need extra expansion slots or ports. Performance features aren't that crucial with a HTPC unless you plan on using it as a gaming rig.
The only area in which I tend to disagree with the recommendations is that they're usually either microATX or mini-ITX boards. I like a HTPC with lots of tuners so I need a full-size ATX board for the maximum number of slots. The smaller boards have a limited number of slots so they are of no use to me. I also upgrade the integrated Realtek NIC with an Intel gigabit NIC, which requires another PCI-e slot. Throw in a pair of Ceton InfiniTV4's and a couple of dual ATSC tuners and I'm already up to five PCI-e slots. Most boards these days only have 4 PCI-e slots or less so my choices tend to be somewhat limited.