I agree with DalekJim about Ghost Light incidentally. If it wasn't for The Curse of Fenric it would be the greatest McCoy story, and is a very, very close second.
Fenric made my Top 10 TV Who Stories in that thread I made a few weeks back. Both Fenric and Ghost Light are very complex, multi-faceted stories. I find them a real antidote to a lot of the modern sci-fi out there that is practically screaming with pride about how dumb, cookie cutter and simplistic it is (Hi, Jar Jar Abrams!).