The bigger the fan, the more are that can be moved at lower speeds. I have 2 120mm fans in my case running around 1600RPM and they keep it cool. Now when I crank them up to around 4000, they scream, but then it REALLY cools down this sysem.
Another thing, if you're into keeping noise down, larger ones tend to be more quiet. Now, if mine weren't on a controller, I certainly couldn't stand how loud they are on full blast.
Something else I found out, which this might be due to my case layout, I donno... But my case seems to get coolest when my rear fan is full blast and my front is at it's slowest speed. When I have them both going fast, the temp rises!