I get annoyed when I see people slating Voyager as being the worst Star Trek. For a start, it makes me think they haven't ever seen Enterprise, which really was the worst of the franchise -- although even that show had its moments.
I liked Voyager because it was pure Trek. What I mean by that is set on a spaceship, not a space station -- DS9 could have had the best stories, but without spaceships it just isn't Trek. Voyager also had the advantage of an ongoing storyline, namely the crew's efforts to return to the alpha quadrant.
What's more, the storylines -- excepting the occasional stupid time-travel or holodeck yarn -- were excellent. From season three onwards, the series rarely misses a beat and the excellent character development between the main crewmembers is excellent. Watching Janeway slowly accepting the holographic doctor as a part of the crew and granting him the same rights as everyone else is a particular pleasure. As is watching the relationship between Seven of Nine and Janeway blossom, and at times fall out in the most spectacular way.
I think the brilliance of Voyager has much to do with Bryan Fuller, who started as an occasional writer for DS9 and was heavily involved in Voyager as a writer, script editor and eventually as executive story editor. Fuller is nothing short of a genius and has gone on to create shows such as Wonderfalls, Dead Like Me and the phenomenal Pushing Daisies.
All that remains now is to see if JJ Abrams can do something interesting with the re-imagining of Trek that's in production currently. If he does a good job, we could get another Trek series -- and maybe it will be nearly as good as Voyager.