I think Blink of an Eye will always be my favorite. I see it as the Inner Light of this series. And yes, I know the story was ripped off, but it was ripped off really well!!!
I'm not a die-hard Voyager fan, but I have to go with Real Life. It's easily the best holodeck episode in any series that had holodecks, and it also goes far enough outside of the box to be genuinely interesting, and to compete with the best of TNG. I can't understand why this episode is cited on its Memory Alpha page as receiving poor reviews.
Really, guys, Timeless? Starring the two dullest cast members/characters, massive TPD violation, and a Galaxy-Class ship without a Galaxy-Class bridge? Not saying it's terrible, but surely the series did better than that. Now, I'm no Voyager expert by any means, having seen only two eps, I guess, over the past five years or more... so, here's my shot in the dark: Flashback. 'T'was badass.
I'm going to preface this with an admission that might 'lessen' my status as a Voyager fan in some people's eyes: compared to both DS9 and TNG, I've only ever seen the series 'in chunks'. Having admitted that, my choice for my 'favorite Voyager episode of all time' goes to "Think Tank". My favorite aspect of Think Tank is its storyline, which really gives Seven a chance to shine as a character outside of her role as a 'former Borg drone who still acts and thinks like a Borg' and also really hammers home the depth of connection that exists between her and Janeway. I also really like Jason Alexander's role in the episode; I became a fan of his due to the voice work he did in Aladdin: The Return of Jafar and Aladdin: The Series and his role in Disney's live-action production of Rodgers and Hammerstein's Cindrella, so it was great to see him show up on Voyager. Plus, his character really reminds me in many ways of John Delancie's Q. Note: I haven't seen either of Delancie's two appearances on Voyager, so the above comparison is being made based solely on his multiple appearances on TNG and his lone appearance on DS9.
Someone to Watch Over Me. It focuses on my two favorite characters, The Doctor and Seven. I usually don't go for episodes like this one, but this one was really well done, and had a lot of emotion and humor to it.
"Cold Fire" Spooky, exciting with Kes as the main character. Shows how Kes is tempted by evil forces but overcomes them and finally saves the ship.
Ugh, I love "Muse" so much. I make sure to never miss it when its on. So inventive, creative and well acted.
How about a top ten list? One is so hard to choose. There are at least 8 right off the bat that I love... the ones I can watch over and over and never tire of them. A top ten list would be really fun!
My favorite episode is Blink of an Eye. I loved the concept of seeing a civilization growing right in front of them, sending the Doctor down to the surface for three years, and how cultured he was when he came back. The race that wanted to blow the skyship out of the sky, and evolves to a technical ability beyond that of our Intrepid starship. Fantastic episode. I also relate it to the TNG episode Inner Light, as a previous poster mentioned above.
I think my favorite episode of Voyager all Time is Before and After. It featured my favorite character with my favorite hairstyle (Introduced in this episode) and it was a bit of a twist on the time travel story. While Warlord gave Jennifer Lein a chance to shine, Before and After gave Kes a time to shine and it was absolutely fantastic.
This hast to be without a doubt The Year of Hell. It has a very engaging and gripping story about Annorax and his time ship, and he changes timelines and all of that just to get his wife back. Powerful stuff, and the more you think about, the more crazy you realize Annorax is. He has brought billions of people to life, then killed them again, and brought them back again. It's crazy. Also we get to see Janeway very hard as nails, as she does all in her power to keep Voyager in one piece. It's such gripping stuff, and the ending, ramming Voyager into the time ship is so awesome.
Have you seen froot's vid? http://www.youtube.com/watch?v=ocfZJnnyIt0&feature=player_embedded [yt]http://www.youtube.com/watch?v=ocfZJnnyIt0&feature=player_embedded[/yt]
I used to own Scorpion and Year of Hell on VHS back in the day, and watched the hell out of them. They were always my favourite episodes. Some other episodes that I remembered I loved when I rewatched the series are Deadlock, Muse, Timeless, Barge of the Dead, and Latent Image.
Just beginning season 6 now, but so far my favourite episodes are - Worst Case Scenario and Bride of Chaotica! but also for some reason I really like the 37's, always cheers me up on a down day.