I can't possibly pick just one... but if I was FORCED to, it would be season 6's Barge of the Dead. One of the reasons I love it was that it culminated a year long dance / estrangement
/rapproachment between Janeway and Torres.
I would throw up my fav final scene from the ep, but I've been accused of liking that scene as much as Chandler and Joey liked porn on "Friends".
Yeah I would have to do some digging around and serious thinking before picking ONE episode. I could probably list my favorite episode by-character or pairing easily though.