Neelix, Tom Paris and Barklay, but none more than Neelix.
Having just finished the series, and yes, somewhat disspointed with the final episode, none the less, it remains my favorite of all five incarnations. It sure beats the finale of TOS, ha ha, or Leave It To Beaver--have you seen that? Ward and June look through a scrapbook and then Kennedy is shot.
Neelix and Barclay are the theme of the whole series; discomfort, fish out of water and overcoming difficult circumstances. Tom Paris, looks the most like Captain Kirk, but always reminds us he is not, a Captain Proton fixed, sometime troublemaker, he learns to become a man and a father, an excon, falling short of parental expectations. He is a more realistic persona.
Things didin't always work out on this series the way we might have hoped or imagined, but I think that was part of the point of it. Neelix and Barklay represented this theme along with the beautiful Seven. What a tragic figure (hinted at more with the 23 years timeline Grandma Janeway erased) and genuine character she was. My first impression of her was she was strictly about sex appeal, but that would be a view held by casual, cursory glances at the show. Seven shared in the theme of a fish out of water along with Barkley and Neelix. The point of Seven was for all of us to see past her outer person and into her heart, again and again that theme is repeated, probably to little avail, but they tried. She is a real human being, not a cyborg or a magazine image. Can't she understand how much I care? Okay, sorry. Easy boy.
The "real" final episode of Voyager, for me, an episode with a more cozy, happy ending, was a few episodes back from Endgame where Neelix saves a colony of Talazians. That was more satisfying. I appreciate the writers efforts with Endgame, it was fine, and twisted things around, as most Voyager episodes did, right from the start. But, would it be that hard, to CG in a special edition ending, where we get a ticker tape parade? I don't think so.
To me, Neelix, is what Voyager was all about. The dweeby fans maybe?, the outsiders, the non-starfleet folks, the Barklays of the world, the unsong heroes, who never quite fit in. Hip folks like Janeway and Chokotay became the heralds of a misfit crew's journey, their story was almost secondary. But, in their own way, they were outsiders too.