In addition to the PyMOL manual, the built in demo, and this handy list of over 600 settings, there seem to be a fair number of tutorials for PyMOL.

Which would you recommend and why?

As a starting point, a simple use case might be to visualize the amino acid location of a somatic mutation in its 3D context, and label/mark a series of such positions.

Of course, feel free to advocate something other than PyMOL as well...