There's the story I found totally offensive, from a writing point of view, not what it dealt with. That gets its own special post. There were probably worse stories, but this was the one that stopped me watching. I came back when the brought in seven of nine because I wanted to see how they handled that, and kept watching.

And the series itself, which I thought wasted all it's potential, get a post.

I honestly believe that over and above any other Star Trek series Voyager had the most potential to be mind-bogglingly brilliant sci-fi TV. Two crews with opposing ideologies in a single ship, seventy years from home in a totally alien part of the galaxy. With modern television effects and the Star Trek franchise strength to allow you to really stretch and tell stories that would be to controversial to tell on another series.

I would club baby harp seals for the chance at something that good.

Voyager occasionally produced a great story, but more often than not, produced weak stories. That said, it was rare that a Doctor or Seven of Nine centric story was crap. Most were at least good, many were excellent.