I'm building a HTPC case for this board, and and trying to figure whether it is best to make as much of it out of perforated aluminum sheet as possible for max ventilation, or should it be designed to "chimney" the heatsink and create a more channeled, higher velocity convection pattern.

Another issue is whether to use a single 2tb green drive with a system partition, or put the system on an 80gb 2.5" drive I have sitting around. I'm not sure of the benefits of the latter, since there's not much the HTPC will be called upon to do that doesn't involve data read/write, Netflix streaming will mostly be handled by the smart TV, only Hulu & other website streams will be via the HTPC.

Thoughts?

There aren't a lot of chimney cases. I don't know if it'd work with a board that doesn' dissipate much heat to begin with. But I can tell you that metal with lots of big holes on all sides works well. Make sure there's no obstruction and a bit of clearance so that air can rise totally unimpeded from the heatsink.
Some heatsinks work better in some orientations so you might want to test that before building.

You could use a cheap USB Flash drive instead of a 2.5'' drive for the system or use a RAM drive depending on your OS. The point is being able to spin down the main drive. But if you're going to put the box on standby (or even turn it off) when you're not using it, there's little point in doing any of this.

I built a HTPC using the Atom/Ion counterpart to that board. (the at3iont-i deluxe) I learned a few things that I wish I'd known before I started. Here's what I can remember, that you might want to consider.

My original plan was to cool it passively. But, just to see what would happen, I put a 500 RPM fan on the MB heatsink. The heat output of these boards is so low that that one little fan brought the board down to nearly room temperature. Making things fanless had been my biggest concern, but when I actually put it together I realized that this fan was inaudible, and made it so heat was not an issue at all. So I kept the fan in. The case was the perforated kind, which worked very well.

Will this HTPC have an optical drive? In a machine this small the optical drive might generate a large part of the heat. Power usage on my machine jumps from 20 W to 30 W when I'm using the DVD drive. (It's a full-size drive. I wanted a certain model because I knew I could make it region free.) Unlike my mainboard, the optical drive does not have a giant heatsink on it. The DVD drive needed more ventilation than I had expected. DVDs used to come out of the drive hot. I don't know if that's normal.

Is your goal with the two drives speed or silence?
I second HFat's suggestion of putting the OS on a flash drive.
These drives might be the loudest thing in your system. If the case is perforated, sound from the drives will be more noticeable.
I don't know what shape your case is going to be, but if I were building one, I wouldn't put perforated metal around the drives if I could help it, and I would let them sit on some kind of foam.
Of course, there's a lot of variation in how noisy these drives are. One of mine was not so good. Maybe yours are better, so you won't need to worry about this.

Good luck.

Thanks for the feedback. Here's the plan, a base and face of MDF, a perfed AL cover, the MB on 2" standoffs over the DVD and the HD on an elastic suspension. I think the heatsink is designed to work best flat like this, it's a bit more elaborate than the Atom version and I doubt it'll need a fan. The case could be a little smaller, but it's fine for the bookshelf it's heading for. The EADS drives are pretty quiet, and as this is a dedicated HTPC that might be used for websurfing from the couch, the speed to stream video seems ample as configured. I don't see why I need a back cover at all. The DVD under the MB is probably not optimal, but there's not much choice, lofting it over would be a big PITA. I just hope that the open design takes care of the heat.

Looks good. I assume you're going with a pico psu, you don't have any dedicated space for psu in there.

You better test the possible orientations before building. That heatsink is flashy and is probably expensive but that's not the same as being effective. Asus' Pineview boards can be cooled without a fan (it looks like they've got the same heatsinks as their Ion boards). This Zacate board, I don't know because I don't recall any reports of successful fanless operation. Again, better test before building! If it turns out temps are already high outside of a case, you should be extra careful when choosing your cover.
The cover in your drawing looks like it'd impede airflow too much. You might also want to have a bit more clearance above the mobo. FYI, using Asus' Atom heatsink my CPU load temps jumped 11C when I closed the cover of a Morex T3500.

While I couldn't find any anecdotes about orientation performance, Newegg did have posts from people successfully going fanless on this and the sister PRO board with a less elaborate sink. What I couldn't see until I took delivery was that the heatsink is 2 layers, the vanes of the top at 90 deg to the bottom. So while flat, the air enters the bottom sink at the ends and rises into the top sink's vanes. But on end, the bottom layer is not allowing full vertical convection flow. But maybe it's enough with such a big heatpiped sink. And that cover is aluminum perfed with 1/8 holes on 3/16 centers, 40% open space. You don't think that's enough?

I don't know what your numbers are so I don't know how big the holes are.
Regardless, of course it would work. The issue, as always, is what kind of load temperature would you get. If you're comfortable with high temperatures, don't fret.
But if you want moderate temperatures, test the board's heatsink outside of a box and see how close that temperature is to the edge of your comfort zone. My guess is that you can do better than that pattern when it comes to the amount of open space if not the size of the holes. But I don't have a physical model so it's been trial and error for me and that process could easily have led me to misconceptions. It only matters if the heatsink doesn't work all that well without a fan to begin with anyway.

I'd be nice of you to post your temperatures for future reference by the way.

Will do. Can you recommend the best way to log them? Last time I got into this I used Speedfan. Is there some better program, or just use the BIOS?

What OS are you talking about? And do you want actual logs/graphs or just a few measurements?
I usually use Open Hardware Monitor on Windows and lm-sensors on Linux. But it could be OHM doesn't support Brazos or that there's no appropriate kernel modules for your version of Linux. The developper of OHM is responsive so report it if you ever try it on unsupported harware.

Taking a couple of measurements of BIOS values is generally useful because it's a software-independent reference people can use in comparisons.

So the HTPC is up & running. It ended up with a full load temp of 60 in a 77F room. But that meant at least 70 if the AC was off (it's been hot here in NJ), and that seemed just too high. So I sat on the heatsink an old 40mm fan I had from a P3 cpu, which using the Asus fan software set to silent runs pretty silent at ~2k rpm and keeps it down to 45 or so. Oh well, it's hugely better than my old Celeron HTPC in a full size ATX case with a 120 & 80 mm fans going. Even with them turned down that sucker was loud.

Was it worth paying a little extra for the fancy heatsink? I don't know, but the board has lots of nice features besides being tiny, like built in wifi, bluetooth & USB-3. I don't turn over my hardware very often, the last HTPC build was nearly 6 years ago, so it made sense to spend a little extra.

It's been a little bizarre trying to get the screen settings to a comfortable viewing on my new 46" screen from 8' away. I've set text res to 200%, and Firefox zoom to 170%.

An interesting article came out for couple of fuision boards, seems the Zotac has better passive cooling, power consumption and cheaper than the Asus, Anandtech Fusion E-350 Review: ASUS E35M1-I Deluxe, ECS HDC-I and Zotac FUSION350-A-E

The design of the Zotac's heatsink looks more sensible. It is unfortunately not cheaper here, making it poor value (like the Asus). Maybe that'll change with time. Newish parts are often overpriced.

Honestly, I don't know much trust should I put in those numbers, since I type this post from a system which draws typically less then 15 W from the brick.

The numbers themselves are useless. The review says so. But the differences might be about right.

And if they are, they're really rather minor given the nature of what these systems are being built for, both taskwise and pricewise. If one is wanting to overclock and game, why look at a Zacate to begin with? And in the context of a new build, $175 vs $150 vs even $125 isn't that big in the overall picture.

Yeah, especially since Anandtech has claimed much better efficency for a cheaper Zacate boards (I'm somewhat skeptical).