10. Second Doctor - The Krotons (1968)
This story is taken from Patrick Troughton's final season. The Krotons aired four episodes from 28 December 1968 through 18 January 1969, and is particularly notable as being Dr. Who legend Robert Holmes' first scripted story. This serial follows the Second Doctor and his companions Jamie and Zoe as they meet and interact with the native Gonds of the planet (who unsurprisingly look and sound like 20-something British actors). Eventually though, the Doctor and company learn that the Gonds are ruled by mysterious and unseen Krotons, who conduct frequent surveys to find the most intelligent of the Gonds. What makes this stand out to me though as being the worst Troughton episode is really just three things. The first being the look of the Krotons themselves, when they're finally revealed (see above pic). Doctor Who made an impact originally because of how it tried to avoid the stereotype of science fiction at the time, namely having monsters that were just guys in cardboard suits. But for this story, its like they just gave in. Secondly, comes the acting: while you can always count on Troughton and his companions on delivering a good performance, the supporting cast seems lifeless and uninteresting, despite having a few notable guest stars (mainly Philip Madoc). And third, the pacing is all off. Practically nothing happens in one episode, while the next jams in too much. Still, seeing as it was the first time for Robert Holmes, I think this can be overlooked, especially considering the amazing scripts he would turn in later in his career.
If You'd Like a Good Patrick Troughton Story: It would be criminal to not refer you to the amazing "The Mind Robber", or the best Cybermen story ever "Tomb of the Cybermen". And if you've got patience, try the epic 10-part serial "The War Games", also starring Philip Madoc.