And as mentioned, damping just the top panel is not enough; you probably have to add mass damping to almost all the panels.
Absolutely, the acoustipack kit (which seems to have been discontinued) covers all the panels including underneath the motherboard. But yes, ultimately aluminium is not a good starting point.
Unlike desktop cases, the size of an HTPC case (particularly it's width) is limited by it's intended environment (i.e. hi-fi cabinet/stand). Having examined several HTPC cases in person I don't think that there will ever be a perfect case to satisfy the SPCR crowd. Part of the problem is that quiet components are only available in standard sizes and they take up a lot of case space which in turn impedes airflow. We are starting to see 2.5" hard-drives as a viable alternative, but other things such as near silent CPU coolers, optical drive, HD capable graphics card, PSU, etc. take up a lot of space
The good news is that with the imminent release of chips with much lower thermal profiles (Prescott, you shall not be missed), near silent heatsinks can afford to be smaller. Intel have also promised that their next gen integrated graphics part will be HD capable (as well as being HDCP enabled). This in turn should greatly reduce the need for powerful PSU, so maybe manufacturers will take the opportunity to make small PSUs with S12 type acoustics (or maybe picoPSU might come into play).
Of course there is the other alternative, and that is to use VIA cpus and the like, and that's a viable option. However these are not suitable for the full MCE + Extender experience.