Lot's of different factors to consider when it comes to coolers.
As you shorten the Z height, you tend to need to extend the X and Y axis to make up for the loss of surface area for cooling. Therefore, the heatsink may crash into other components on the board like the VRs, etc.
So this may in part depend on what board you are using and whether or not there are heatsinks on the NB or VRs.
I have used the Noise Limit silent flux media cooler and it does a pretty good job and is relatively quiet. http://www.directron.com/3100003.html
The Shuriken from Scythe is also supposed to be pretty good.http://www.newegg.com/Product/Product.aspx...+USA-_-35185129