I agree (to some respect) SMALL fans are next to useless. I have a KD7 board and that came with a 40mm fan on the NB. After a month it the noise from that was appauling, so I replaced it with a
Zalman chipset cooler... my mobo temp actually went down by 10*C with the added bonus of chipset cooler that doesn't make noise.
I don't think I'll put it on the water cooling loop... IMHO it just isn't worth it... plus it'll heat up the CPU too much.