Having seen a significant portion of Star Trek episodes (All of Next Gen. and 6 1/2 season voyager and a season of enterprise) I already have favorite episode arcs.
Borg - love them, despite their predictability they are great
Time travel -particularly those where they end up in the 19/20/21 centuries
Anything Klingon - possible the worst race ever conceived, really difficult to assume that such a race could have made it out into space
Spiritual ones - including Vulcan ones, another race i see as being unable to evolve in any form.
What are yours?