3mm?
Oof. Yeah, I'm not too surprised to hear that. It's a really small case, and that ASRock board is fairly unique. I certainly haven't seen any other boards laid out in that way. There are a couple of other options that still give me the mSATA;
this one is just about the same. And there are Intel options too, I just like ASRock (current mobo has been incredibly solid.)
Maybe I'll come up with a custom case idea?

Regarding power; yeah, I am definitely thinking about a
picoPSU with an external brick. I'm only running an i5-2500k, built-in graphics, and one (maybe two) ssd (hence my interest in the mSATA) so power demand isn't going to be tremendous, even at full load -- even if I overclock the i5 a bit. 150 watts should more than cover it.
I'm shooting for the best balance possible:
small form factor (the m350 case)
speed (the stock i5-2500k can handle everything that's currently playable in MAME, in addition to PS2 emulation)
and
"silence" (the new
Noctua NH-L9i, which is the biggest question mark at this point, because no retailers have it to buy yet. If that guy's tests are accurate, though, this heatsink will definitely do the job - maybe not perfect, passively cooled SILENT ... but very, very quiet. Especially since this system will hardly ever be really pushed to the thermal limits.)