Here is a "sushi inside-out roll" hybrid approach: A Streacom NC2 passive case, with an external 120mm fan undervolted to run off 5V USB power. Look at those chunky, deep case fins; this approach is a natural idea with this case. It might not work as well with other cases.
I'm running parallel computations that needed the BIOS watt and amp limits doubled, to not throttle (other web sources have never seen these settings affect CPU performance, only graphics, so I'm truly loading my cores). My core temps are 50 to 55 C, depending on the fan, compared to 70 C without a fan. One only needs to move the faintest amount of air to make a huge difference in how this case cools, so the choice is entirely about fan acoustics. My favorites are virtually inaudible.
One could also attach an external PWM fan to the internal PWM header. Note that it's a very small header, perhaps the same standard used with graphics cards. One could cannibalize the cable from the stock internal fan (shown above). Note that the fan power rating exceeds Intel's rating for the header, 0.25A. That's plenty for an external fan; I'm getting good results with an 0.07A Scythe Slipstream.
Note also that this is a 5 VOLT fan. Huh. My PDF manual for the D54250WYK says nothing about the fan header voltage. An ordinary 120mm (or 92mm or 60mm) PWM fan is likely to start up and run on 5 volts, but be prepared to experiment. Similarly, not all 3 pin fans start up on 5 volts USB. Some need a flick of the finger (like an aviator giving a prop a push in old movies) but then run ok on 5 volts. Best bet before ordering fans to experiment with is to watch one of those Youtube videos where they adjust a variable voltage supply and you get to watch the fan for yourself.