Hmm, hard to point out a single "favorite" but I'll just list off some I liked a lot.
Living Witness... campy fun with the "warship Voyager' and a great story about the Doctor.
Tinker Tenor Doctor Spy... this episode always makes me smile. Lot of silliness about the Doctor's fantasies, and sure he's humiliated when it comes out, but in the end he gets to play the hero and save the day after all.
Blink of an Eye... I liked how we got to see the evolution of a whole species all in one episode. It captured a real feeling about looking up to the sky and literally reaching for the unknown all with a happy ending.
Distant Orgin... space dinosaurs! How cool is that? Sure they're jerks, but most aliens in Trek are, so why not? Fun stuff.
Death Wish... easily one of the best Q stories in the Trek franchise. The only bad thing to come up with this, it was so successful they just -had- to make a sequel which was epic fail.
None of the ones on that list made my favorite lists, but if I had to pick one... Scorpion. Not because of the Borg/8472 bit but because of the Janeway and Chakotay conflict. The tension and drama between the two really carried the episode for me. This is what we should've been seeing more of to make the show really great. I also liked Timeless a lot though. Amazing they crammed that much action into a single part episode -and- made the future Kim and Chakotay seem interesting!