I assume you want to build your own Micro-ATX case, for instance in order to create a small car computer, which is a thrilling idea to me. If you were asking for the smallest commercial case available at shops, this question would have been closed.
First and most important, you didn't disclose your space constraints in the question. While I still believe that the question, as is, is a low-quality subjective question, I'll try to give you an answer.
Computer hardware is based on standard sizes for components. Any component you can remove on your custom design may help you save space. In a few words you have to install: a motherboard, a PSU (unless... see later) and a hard drive.
OK, since you don't need PCI/x cards you can save lots of depth according to the case I just saw on your link. At the current time, we are trying to make your case be as deep as the metal plug plate (I don't know its exact name), which is provided by each motherboard vendor to match the mobo's specific connector layout (PS2, VGA, etc.) and has a fixed size. If we can go no deeper than this we saved lots of space.
Problem 1: PSU. PSUs are standard. Unless you build your own or have an external power source with 24 rails, which is very difficult but feasible on a car design, you must install a commercial PSU that returns to the standard depth of the case. In case you remove PSU from its seat, you also save height of your case (let's keep in mind the one you linked).
Now hard drive. You need just one... OK. If you are ok with a SSD which is generally smaller it's time to think about where to place it. Perhaps you need to build your case with a special HDD slot on top, parallel to the motherboard plane. This assumes again you don't use PCI/x cards. This time the total length of the case matches the motherboard's, but perhaps you need very little more depth to host the HDD with sufficient space.
Problem 2: heatsink. How high is that? Since it's perpendicular to the mobo's plane, it adds depth to the case. Don't forget it. Use the smallest heatsink you can find.
Thoughts
I am unable to provide you with exact dimensions of the smallest case human mind can design. I have tried to provide you some hints on how to design it. Unfortunately I believe your question is still too subjective. I have tried to answer but again my answer is subjective too. I'm not deleting it because my advices could be considered valuable.
1Are you going to build your own Micro-ATX-compliant case? – usr-local-ΕΨΗΕΛΩΝ – 2013-03-04T12:33:06.743
1@haziz: If you're looking for it to be as small as possible why are you choosing Micro ATX over Mini ITX? Also this is basically a shopping recommendation which is off-topic. – James P – 2013-03-04T12:49:07.340