Encaitare has me thinking of Gothmog.  There are times when PJ does some trully wonderful stuff, and I think stands out as a director.  For instance:
Eomer finding Eowyn, just the look on Karl Urban's face.  
 
 
The interactions between Denethor, Boromir, and Faramir.  Also, between Pippin/Gandalf, Faramir/Pippin, Boromir/Faramir...etc.
Sam's character in ROTK.
For a personal favorite, I love the connection PJ draws to Isildur and Frodo:

Look at the simularity in their faces.  It's moments like this when I sit back, and say wow PJ, that was great.
Then there are just times when PJ sinks back to his C rated gore movie crap...
The meaningless beheading of MoS, and mutilation of Gothmog.  There is absolutely no point in these two sequences except to add blood and gore.