We wanted a case that would blend well with other A/V components, provide minimal visual distraction, and support our current Micro ATX motherboard and possible future full-ATX upgrades. Zalman's HD135 fit the bill, with an appearance similar to 17" by 5" home theater receivers.
Its mid-sized appearance is a bit deceiving however, as an extended power supply section allows full-sized parts to fit in the traditional orientation.
Alternatives are available from traditional full-line case manufacturers, as well as HTPC specialists such as Ahanix and Silverstone. Buyer beware, however: the slimmest cases use riser cards for expansion slots, narrowing motherboard choice to those with matching slot positions.
When it comes to CPU cooling, bigger is better; large coolers are able to do the job at slower fan speeds, creating less noise. Height restrictions, however, prevented us from selecting vertical coolers such as Zalman's CNPS9500 LED. Fortunately we had Sunon's new Waturbo Liquid Circulation Cooling System on hand.
The Waturbo uses a small impeller under the fan motor to circulate cooling liquid throughout a chamber in its center. Besides bringing heat from the base to the top of its sink more efficiently, the pump and seals effectively prevent rattling noises as the bearings "break in".
Note that while the "best choice" for any given chassis tends to be the largest cooler that fits, but it's still important to read cooler reviews for details on fan noise and cooler performance.