IMO blu ray is still the main problem area of HTPCs.
I was going to go for a mitx ion board for a HTPC, but the HDMI can still not bitstream HD audio. Given the single expansion slot is going to be used by a TV card, it's not a viable option. In the end I went with a micro atx board with HDMI output (video decoding and pass basic audio) , with a view that I have sufficient expansion should I need a soundcard or graphics card, whichever way it goes to best make use of the format. Currently the only options afaik are the top end ATi cards (overkill for a htpc, not to mention expensive) or the HDMI soundcards (again, way too expensive).