wow - that is a surprisingly thorough introduction to thermal transfer. Based on your experience, to increase thermal transfer would you want to dimple the surface or add protrusions? (I know, at the extreme these are almost the same thing). I was reading golf ball dynamics and not sure if it applies or not.
Both of those ideas work to varying degrees. You can "trip" the airflow at the leading edge of a heatsink fin by introducing notches and protrusions of different geometries. This will make the airflow past that point turbulent for a certain distance. Depending on geometry you might have re-attachment, which leads to rebuilding the boundary layer. Dimples and surface roughness can help too.
In the end you have to deal with the real world. Some of these techniques are really good to grab dust in the airflow. If that happens, you have, ultimately, created a problem greater than the one you started out to solve.
After all I've been trough I have become a huge proponent of fluid based cooling. I don't think there's any way to have forced air cooling even begin to compare with the potential performance gains of using liquids to mechanically move heat around.
http://www.aerospaceweb.org/question/aerodynamics/q0215.shtm...