Sounds like you're determined to go mATX, which is what my dad is using (and I have the same motherboard in my primary desktop - Asus P5N-EM HDMI), and the form factor quite decent if you choose a motherboard with some good audio and video options. If you won't have many expansion cards, then you can go for a low-profile case as well. Just be careful since a focus of HTPC is small + cool + quiet, and these things are often in conflict so expect to do a lot of tweaking once you have the main system all built up. As
trivial has already mentioned, the CPU cooler should be one of the first things to be changed, but make sure it will fit inside your case - i.e. will it be blocked by the PSU, etc.
Have you considered mini-ITX though? Your options are few, but there is only a handful of boards you need to look at. But this is where you have the ability to build really tiny systems that you can just hide away somewhere.
Here's a setup I built recently:
Zotac GeForce 9300-ITX WiFi motherboard
Mini-box M350 case
PicoPSU-150-XT power supply w/ 102W power brick
Intel Core2Duo E7500 2.93 GHz (had a Pentium Dual Core E2200 2.2 GHz earlier)
G.Skill F2-6400CL4D-4GBPK RAM
Seagate 7200.3 320GB 2.5" 7200RPM HDD
...and a couple of fans attached externally and a $130 USB Blu-ray burner from eBay when I need an optical drive. I am a huge fan of this motherboard, since it has the potential to be upgraded with some really high-performance parts but it's no slouch with even the onboard components. If you are only interested in media centre stuff though, I think the Zotac IONITX series may be of adequate service as well.
I highly recommend an actual HTPC over a media centre, you will really appreciate the versatility, like being able to run BitTorrent :p
And about what I said about hiding away the tiny system, I have mine hanging off the VESA mount behind my monitor completely out of sight. Take that, iMac.
The space inside the m350 is really tight, and I can only fit one 2.5" HDD with the stock Intel CPU cooler. I'm waiting for a super low profile cooler from eBay, and I might be able to squeeze in another HDD, thinking of getting SSD for my system drive. But if you go the mini-ITX route, you might be better off with a more featured case like an Apex MI-008 which will let you install a standard 5.25" optical drive.
Anyway, I get a huge boner for system builds, so do keep us updated...
). I know what kind of hardware I'd use (microatx). I'm more interested in the pros/cons people here have had with home theater PC setups.
