Generally, harvesting from primary will get you more generations of suitable yeast. What you are doing is putting a selective pressure on the yeast, i.e. you are mimicking natural selection. By harvesting from the secondary, you'll end up with yeast that essentially has lost the ability to flocculate. Primary yeast is a lot more diverse, giving you a blend of early, "normal" and late flocculators, hence it is preferred for harvesting.
The Fiesty(sic) Goat Brewery est. 2007 & Clusterfuggle Experimental Ales est. 2009
Primary: Saison, Berliner Weisse, sLambic I, sLambic II, IPA, 70/-
Secondary: Orange Blossom Mead, Flanders Red I
Kegged: Fat Man Porter w/ 1469, Fat Man Porter w/ 005, Centennial Falcon w/ Conan, Centennial Falcon w/ Denny's, Barrel-aged Fat Man Porter, Belgian Dark Strong, Dark Mild