There are a few, but the one that always comes to my mind first is in "Timeless", where Harry figures it out in the nick of time and saves the day - having just been berated at by the EMH. The follow-up scene with Janeway is pretty awesome as well, but Harry's "YESS!!!!!!!!!!!!!!" at the last split second was pretty frickin' cool. Here's the Kim/Janeway bit:
I always liked the scene in the 37s when the crew decides to stay with Voyager...and the one in NIGHT when they all mutinied, refusing to allow her to go off on her on.
SFDebris noted the unintended message: if you suffer severe brain damage you wind up acting exactly like Neelix.
One thing I like that is spread across many episodes, is that pivotal decision that Janeway made to destroy the Caretaker array. Of course, it's the decision that made the series. But on principle, it's clear many people didn't like it... that Janeway compromised her crew for aliens they knew very little about. I would have preferred that Janeway tried to use the array but something went wrong and they ended up stranded anyway. One could still attribute their being stranded to Janeway hesitating on her decision... but it wouldn't be so final, so committed. Yet, we see as Janeway gains experience that she has at times come to regret her decision, especially in desperate times where it looked like the crew and ship was finished. A late-in-the-game moment was in Shattered, where Chakotay informs an earlier Janeway of the stranding in the Delta quadrant... and you can see how she wants nothing more than to prevent it from happening. In the end, she does get her ship and crew home. And her decision touched the lives of millions along the way, mostly positive. Think of the billions of lives saved because the Krenim were stopped, just to name one. So, while it was an exceptionally long "mission", it was a success. And so many people were better for it. I confess that I didn't care for Mulgrew in the beginning, but once season 3 came around I could see how she was bringing about a fascinating personality in Janeway. She did a great job and kept getting better as time went on. I've seen some interviews with Mulgrew and it sounds like she was extremely committed to the series. Very professional. She was more than just the captain -- she was a motivating force driving the other actors as well.
A few times in the latter half of the series, we saw a return to previous moments in time. Either flashbacks or actual interactions with the past. And there is Seven of Nine as a drone, in her original Borg suit. I've often thought about what Ryan must've gone through in makeup to return to that. How uncomfortable that must've been... and that she probably looked forward to returning to the catsuit, despite its discomforts! We also see earlier moments of Janeway with her hair up in a bun. But... heh... couldn't hide the weight gain. Mulgrew put on a few pounds as the series went on and you can tell she's not quite as lean as she was in the earlier seasons. Not that there's anything wrong with it, but it sure helps differentiate scenes from original to late flashback.
In later episodes, when they had flashbacks of Seven as a drone, I noticed that they didn't try to make her look exactly as she did when we first saw her. I guess they figured that no one would notice.
Some of my favorite scenes in Voyager were just visually appealing. Voyager firing everything she had in Dragons Teeth, the armor being activated in Endgame, Kes walking down the corridor and everything blowing up behind her