I am going to start off with the main villain from the season 5 episode Think Tank. Kurros, the main representative of the think tank, was an interesting villain in that he preferred to use his brains in order to recruit seven of nine into his think tank. He almost got away with it if not for Captain Janeway "breaking" her deal with him. Kurros was an intelligent villain who always wins unless you chose not to play his game like the way Janeway did.
My unpopular choice is The Borg Queen. I like how it managed to get really personal between her, Janeway and Seven.
I actually liked Seska. She was a smart, attractive and manipulative person. I liked her voice as well. I find Cardassians females attractive for some reason.
I was very impressed the first time I saw Species 8472 crawling up the hull.. but that was kind of the high point. I love Seska and the Borg Queen is an enigma that delivers
Kashyk was an interesting bad guy. He thought he had seduced Janeway but Janeway was too smart for him.
I like Robert Knepper as the Vaadwaar, Gaul, in "Dragon's Teeth." I like this episode a lot. Robert has a fabulous voice. Memory Alpha says this about him: Knepper was a regular on the HBO series Carnivàle, which also featured Clancy Brown, John Fleck, and Michael John Anderson. He appeared as the male protagonist of a segment of the miniseries Red Shoe Diaries, who is pulled over and then seduced by a female police officer played by Denise Crosby. He also appeared in villainous roles in the feature films Hitman (with Timothy Olyphant) and The Transporter 3. His best-known role is that of the sadistic convict "T-Bag" on the popular drama Prison Break, which featured Wade Williams, Michelle Forbes, and John Billingsley. He was also featured in the George Clooney-directed film Good Night and Good Luck which featured Frank Langella, Ray Wise, Glenn Morshower, and J.D. Cullum. He was a regular cast member on the NBC drama series Heroes (during the fourth season) as Samuel Sullivan, the leader of a carnival of people with superpowers. Fellow season four stars include Zachary Quinto, Cristine Rose, and Kate Vernon. More recently he made several guest appearances in the second season of Syfy's science fiction series Stargate Universe alongside series star Justin Louis. He also reprised his role as "T-Bag" Bagwell on the 2011 A&E drama Breakout Kings. He also played Wyatt Miller in STNG's "Haven." Rob Knepper at Memory Alpha
Bullshit. He trapped them, then gave them an out, in return for Seven, something which Seven figured out in 3 minutes after being one of the gang. That's the super villain equivalent of "Gotcha Nose!" Not smart. I know it's what Q did, but why not just offer them a way home? Giving Voyager a faster Star Drive, or even Towing them to the edge of Federation Space, or the tank could have waited for a problem to organically manifest like dealing with the Juggernaut or banishing the space beasties chasing Ransom... Hell, a week earlier and we wouldn't have had to put up with the last three quarters of the Fight. Of course maybe Janeway was supposed to be helped out of that weird space by the Think tank, but she got out by her self before they could offer aid. Course: Oblivion: Ditto.
Well Seska is clearly the most competent villain the Voyager crew fought in the early seasons, but Culluh was as dumb as a stump, without Seska Culluh wouldn't have been able to tie his shoes, let alone pose a threat to Voyager. Seska was the only reason the Kazon were threatening at all. I don't think Voyager had as many good villains as some of the other series did, but Seska is a good choice, though I would disagree with Culluh.
Arturis I liked him because it showed that the writers were paying enough attention to realise that Scorpion was where Janeway's character had gone all kinds of wrong and the borg alliance had lead to far more death and destruction than simply using the array to get home ever would have I also like the fact that Arturis was kinda sad.....not cunning, smug or wicked......just deeply upset at the horrible consequences unleashed upon his word by Janeway Janeway has a breakdown in the following episode.....coincidence?
He just killed a few people to save his own life. Janeway destroyed the universe to get home earlier.
I have to mention Varathael, Laazia and Naxor from a very good Voyager book I've read. They were really creepy.