Season Four. It was the season's most consistent. It wasn't as consistent as I would have liked but it was a vast improvement over season three where it was just one crappy episode after another. I think the addition of Seven, the Borg, the three telefilms, the Hirogen arc, the contact with Earth and more control by Brannon contributed to its success.
Season 6 because it contains many of my favourite episodes from the series: Barge Of The Dead, Tinker Tenor Doctor Spy, One Small Step, Pathfinder, Blink Of An Eye, Muse and Life Line.
Season 2! Excellentseason where all the episodes were great except for "Threshold" which is actually watchable if you consider it as one of Janeway's nightmares after eating too much of Neeilx's food. Season 1 and 3 are great too. But I must admit that I'm not too fond of season 4-7. Something very important is missing!
Season 2 thanks to great episodes like "Death Wish", "Resistance" and "Meld". Season 4 would be the close second.
Season 3. Although I liked Seasons 2 and 4 as well. In season 2, all the crap started happening. The show became like a soap opera in that Seska steals Chakotay's DNA and impregnates herself with it. My mouth dropped thirty feet when she told him: "you're gonna be a father" :O SAY WHAT?! Season 4 was consistant and it had a lot of really good episodes: "Scorpion", "Year of Hell". But my favorite season of all was season 3. Most of my favorite episodes were from Season 3. "Future's End", "Basics", "Coda", "Blood Fever".
Overall the sixth is my favorite. The second half of season 2 is a suberb stretch of episodes though.
I voted for Season Five. I'm rather surprised more people haven't. I thought it contained some of the very best episodes, Drone and Timeless being the most notable of them. I thought those were classic. And then you had other great hours like In the Flesh, Counterpoint, Latent Image, Dark Frontier, Bliss, Bride of Chaotica, Thirty Days, Relativity, Someone to Watch Over Me (which was very lovely), Equinox. There were one or two really weak episodes (The Disease comes to mind), but ... that gets my vote. Season Four would be my runner-up. I think, in terms of continuity and ongoing story, Season Two really tried to do the most. They had so many elements running throughout that season (Ensign Wildman's pregnancy, Seska, Suder, alien species hearing rumors of how Voyager was a menace, just lots of plot threads that made it seem like they were really alone and in potential danger). I wish they had kept up that kind of storytelling style. But Season Two also had some weak stand-alones, so ... ... I do think Four and Five, the middle years, were the peak of Voyager, and I have a fondness for Season Five, especially. Though I enjoy all the seasons.