Season 2 highlights:
"Twisted" - There is a great moment at the end of this episode where the crew is literally backed into a corner by a potentially lethal anomaly. Seeing the crew forced to stop fighting for survival is unusual, and it's nice to put an end to the technobabble. It's also fun to see the crew wander lost around Voyager throughout the episode, unable to reach the bridge to even figure out what's gone wrong.
"Maneuvers" - I would watch an entire show based on the adventures of Seska as she schemes her way to power. She's more cunning than the rest of the goody-two-shoes Star Trek crew, and she's a match for Janeway's fanaticism. (Unfortunately, she's mostly pitted against Chakotay, which is less interesting.) Unfortunately, the Kazon are totally sexist or Seska would have conquered the Delta Quadrant.
"Prototype" - A creepy expressionless robot is found floating in space (the design is basically a silver version of the famous Metropolis 'bot). B'Elanna's story arc, moving from intellectual curiosity and a desire to help an artificial species survive to horror at what she's created follows the classic scary-robot story, but is no less effective for it.
"Death Wish" - Love seeing Q, and the moral dilemma is a solid one. I've always thought that boredom would be the worst part of immortality.
"Deadlock" - You'll see this on a lot of best of lists, because it's about as dark as Voyager gets, with an unexpected ending.
"The Thaw" - Yes, this is my nightmare. A tacky, multi-colored world with squawking evil characters intent on holding hostages.
"Tuvix" - This might be one of my favorite episodes. Every time I see it I feel queasy at the fate of Tuvix. The way the crew, who liked him, turn away and leave him to his fate simply because he isn't "one of them." It's chilling, and I wish there were more episodes like this one.
"Basics, Part I" - Remember how much I love Seska? This is why.
Season 2 losers:
"The 37" - This episode pisses away a brilliant question: What if the Voyager crew decided to settle? The fact that they decide to leave a human colony of 300,000 without even trying to recruit anyone seems short-sighted to me, considering that with a 70-year journey they'll become a generation ship. Surely there were some capable doctors with a sense of adventure on that planet! Also, I'm not as in love with Amelia Earhart as everyone else is. Sorry. (Now if this had been about Bessie Coleman, on the other hand....) Still, the last scene where Janeway and Chakotay speculate on who may have chosen to leave Voyager is touching - for Janeway, a validation of her unwavering commitment to going home.
"Projections" - Another promising premise killed by a too-short run time. The resolution feels extremely arbitrary. Maybe the rest of the show is set in the Doctor's hallucination! (It is nice to see Barclay, but he isn't given much to do.)
"Threshold" - One of the WORST Star Trek episodes ever. Extreme ick factor.