Any specific suggestions for mATX motherboards from MSI vs ASUS vs GIGABYTE? What CPU/GPU? Looking for USB3, HDMI, integrated graphics and HD audio, Gigabit ethernet.
Why not consider mini-ITX?
I am building a new desktop and a new HTPC. For both I am using mini-ITX mobos with an H81 chipset. This
article talks about the difference between the different chipsets (Z87, H87, H81). The long and short of it seems to be that there really isn't an advantage for me to use the "better" chipsets since what they offer, such as more USB 3.0, RAID, SLI/Crossfire, Smart Response, overclocking, etc is stuff that I don't need.
My HTPC system will have an HDPlex H1.S case which is totally passive as the case works as the CPU heatsink. I will be using an i3-4330 ($110) CPU - note that the max for this case is 55W CPU. The only drive will be a 120GB SSD, which is probably more than I need, as I have a media server that stores all of my content. The mobo is an Asus H81i-plus.
My desktop will be small enough for most people's HTPC as I am using an Antec ISK300-150 case. This will have a very high end CPU - an i7-4770K ($300) so I may have issues cooling the CPU in such a small case. But I think that the Arctic Freezing 11 LP should be able to do the job as it is rated at 100W. This machine will have a 240GB SSD. It will have a MSI H81i - I prefer Asus mobos but the Asus H81 board did not have optical audio out (aka s/pdif) and I need this to connect to my receiver.
Regarding no info on the mobo's GPU - that is because the GPU is not coming from the mobo, it is coming from the CPU. IMHO there is no longer need for anyone, other than gamers, to get a discrete video card as the integrated video is so good. That means you can get a smaller case and you can get by with a smaller power supply and have less heat generated - all good things. That is even moreso the case if you only have an SSD, even better is you have an mSATA drive.
One other thing - have you considered an Intel NUC? SPCR has a review
of the newest Intel NUC with a Haswell chip. These are about the size of the Mac mini.