This was hard, since "The Alternative Factor" is the series worst, but I had to go with "A Private Little War". Maybe it's because for me the Korean and Vietnam wars were ancient history by the time I was around and watching the show, so I didn't catch the real storyline and didn't really care for it. Plus what was up with the witch priestess in this episode? Was she really trying to cure Kirk or just on to much acid?
But "The Omega Glory" , "By Any Other Name", "The Immunity Syndrome" and "Friday's Child" round out the Top 5 worst of Season 2.