Patrick Troughton is my favorite Doctor. His era isn’t necessarily my favorite, however.
I love what Troughton brought to the role. He is a joy to watch. Every moment he is on screen he is breathing life into the show. His chemistry with Frazer Hines (who played Jamie McCrimmon) is endlessly fun. Even when the show became formulaic in the fifth season with the base-under-siege stories, the actors kept you engaged.
Of screen, however, the Second Doctor is difficult to capture. He is frequently cited as the most difficult Doctor to write for, in large part because Patrick Troughton was so physical in his performance. The way he moved his body and his face is not something that can be captured on the page or in audio. (The audios succeed, however, when Frazer Hines does his Troughton impersonation, which is nearly perfect.) Because of this, the loss of so many of the Second Doctor television stories is a tragedy. The success of the era is due in large part to the performances, and the performances are often visual. There are still some good stories and the recordings capture an aspect of them, but they are still incomplete.
Thankfully, 2013 saw the return of a good number of Patrick Troughton stories to the BBC archives. Enemy of the World is now complete, and Web of Fear is just one episode short of completion. Finding so many episodes together so many years after the archive purge is, frankly, astounding.
Hopefully more will be found.