Hello Winglift,
When it comes right down to it, you only want to run a 3-blader when you want to run an engine whose RPM sweet-spot and max horsepower output, when combined with a "low" pitch, say 10 or 11 inches for good downline braking, would force you to use too big a diameter, just to absorb the available horsepower. The big diameter, combined with the higher RPM, would then cause the tip velocities to be too high, making lots of prop noise (howl). The 3-blader simply lets you absorb that max power level at the same RPM and pitch, and still keep tip velocities down.
The price you pay in decreased prop efficiency (a handful of percent) is more than offset by running the engine in the sweet-spot, rather than lugged-down. If not, stick with the two-blader.

I hope that helps,
Dean Pappas