What works best to clear a clogged toilet?

It really depends on a few things, where the clog is(is it in the toilet itself or in the "stack" below the toilet that runs into the sewer system and what is causing the clog.

For lack of a better way of saying it, if it is toilet paper or a large #2 then a plunger will usually do the trick.

For really stubborn clogs you could use a toilet auger, just pay attention not to damage the finish on the toilet bowl.