When it comes to the boards with limited clearance for the CPU cooler, I can't recommend the Prolimatech Ultra Sleek Vortex 14 fans enough; I ordered one a while ago that finally arrived, and was a bit dubious that the specs were too good to be true, but it actually performs very close to what is promised; extremely quiet, great airflow and strong static pressure. I do think it isn't as quiet as they claim at the higher end of its speeds, but it's definitely quieter than many bulkier fans.
Although I'm using mine as a case fan (since nothing deeper would fit) I'm now seriously considering them for use on all future CPU coolers I get, as you can use them to fit larger heatsinks (with or without better clearance if you need it) without sacrificing performance. Or you could even use them with a dual-fan cooler to improve clearance, both to the CPU itself and in height.
In a well setup case such an arrangement can be pretty sweet; just add a big vent right over the cooler with the fans drawing heat straight out of it from the biggest heatsink you can fit (press the fans right up against the case if you have to, just don't forget some anti-vibration pads if you do). Then add intake vents all around the sides wherever you can, and you have a CPU cooler that's pretty much cooling the entire case.
Sorry that's a bit off-topic, but all I'm saying is that while some of the motherboards are mentioned as having restricted clearance, I've been finding the ultra sleek vortexes can negate that issue entirely. I'd like to see more slim fans like them to choose between, but even though they're currently the only choice they are *really* good. I'm planning to use them for pretty much everything for the foreseeable future