The 4U SuperMicro you linked to is dead silent, I have them in many rack mount and even in my desktop.
The 2U is whiny-loud even at idle, the Dynatron Copper version is much better and nearly silent, it's amazing for a 2U.
The 4U SM won't fit in a 3U chassis.
The 2U SM will, and the 2U dynatron will.
Dynatron R14 = 2U, Copper, and awesome.