Damn you DAN! I was just about to suggest that silverstone htpc case, since I asked about the height. lol
Yeah, look at getting a decent wider htpc case since they still use the slim/half height factor. The good thing is that they use the more standardized micro-atx parts, including a full sized PSU, but you really don't need a lot of power for this setup.
Silverstone HTPC case:
This nets you a pretty nice setup; the case is about the standard blu-ray/dvd player or so and gives you room with 4 expansion slots so you can drop in half height, more powerful gpu along with room for audio cards and such. This also allows you to use the more standard 3.5" hard disks in companion with a 2.5" ssd as well as the normal height 5.25" drive bay so you can pick up a normal optical reader/burner for a lot cheaper than the slim drives. This way gives you room to grow but still fit in on your shelf.
I selected a little more expensive motherboard with this because its the cheapest micro-ATX board that features the elusive 20 pin internal usb 3.0 connector that you'l need for the case; if you want usb 3.0 ports to work on the front. You could grab a cheap $50 mobo and throw in a $30 usb pcie controller, but more often then not, they are a hassle to deal with since nec controllers are known to be flaky to run on the pcie lanes instead of their own dedicated channels through the chipset separately.
Antec mini-ATX build:
For about the same cost as the silverstone build above, this is the true mini-ITX build that will the smallest fully functional pc you can build right now with optical. The Antec ISK comes in 65w and 150w models, but the 150 is like a few bucks more. The best part about it is that its nearly silent since it uses the power brick (picoPSU btw, good stuff).
The case has lots of cooling for such a small case and comes with an 80mm fan included; pair it with the Scythe cooler and you won't hear this thing much further away than a few feet. Shit, you could probably take the 80mm case fan out and only have the cpu fan running... or even just turn it off. Those i3 35w cpu's run very cool and you can just passive cool the whole damn thing.