Voyager: It's definitely hard to give an unequivocal winner. When all is said and done, I would have to give the edge to Seven considering the lengths Janeway often went to save her over four years. Janeway needed to justify her mission to reintegrate Seven into the human community (on her own terms of course) and this drive seemed at times to equal the importance of getting Voyager home.
If one is allowed to bestow special runner ups, I would point to Tuvok and Kes. The loyalty and trust that existed between the former and Janeway was of such longstanding depth that I think one could describe him as her closest friend, however that was actually expressed. Kes was the Captain's dear daughter, a position that was taken in some ways by Seven, but the nature of their relationship was marked by a special poignancy and loving care that distinguished it from any other relationship that Janeway developed. I think if Kes had remained on board for the full ride, I would very likely give her the edge in this evaluation.
As for least favorite, I find this one even harder to determine. I'm not going to take the easy way out and point to a one and doner like Harren. Did she really dislike Seska until she was called out by her who then left to become an out and out enemy as the real leader of a Kazon sect? I don't really see any evidence of that. I don't buy Carey either. Torres was the better choice as Chief Engineer, although it was one made mainly by intuition. Although I liked the character, the senseless death argument doesn't cut it with me. In fact, given the nature of what they do, I think that it is appropriate that one sees this happen more often and not just to the red shirt contingent. In this instance, its carried out in a way that makes it more moving as he was so close to being reunited with his family. At any rate,
I don't see any animus in Janeway sending him on the away team as there was no rational reason to think that his fate, or any of the party's, would have been more inevitable than during just about any other of an innumerable number of missions.
No, I feel that I have to go out on a limb here and say that given the totality of evidence from the entirety of the series' run, I would have to give my vote to Chakotay. I suppose most people would question how I could be serious by even suggesting this. After all their was the genuine romantic attraction that forms the show's main attraction for quite a few viewers. Also,one of the main drivers for Admiral Janeway to pull off her desperate plan of salvation was Chakotay's death, wasn't it?
Well, I think the evidence for my choice was perhaps under the surface for the most part, with some obvious exceptions. Those instances, most notably Scorpion and Equinox, I find not to be outliers that can be explained away by the pressure of the circumstances involved. It seems to me they are simply the tip of the iceberg, rarely explicitly drawn out but present nonetheless. Janeway's lack of respect for Chakotay. I think we are often shown, sometimes obliquely, that while their common desire to get the crew was symmetrical, Chakotay's underlying philosophy of the means and lengths to do so were often at variance with Janeway. I'm not referring to the show's beginnings when his loyalty, being so recently her target of prey, had to be established.
No, I think that his inability to influence her inflexibility in decision making (with one obvious exception) and her weariness in having to deal with it from her senior subordinate, laid the groundwork for her increasing expectation and his acquiesense to accept the role of rubber stamp to her command determinations.
Indeed as time went on, I think that Chakotay's primacy in being sought to help formulate response strategies to situations waned as the importance of Seven's role increased.
Additionally, and this is hard to support directly, I suspect that the intimate feelings that were only given sanction to be expressed in Resolutions, became a source of resentment for Janeway. She knew that the prohibition of any shipboard involvement was inviolable and yet here he was, always trying to be as solicitous as possible, and beyond at times. Wouldn't it have been much easier to master her response and control of her emotional needs if this reminder of the lure of not being straightjacketed emotionally was literally almost always by her side? Of course, there are those who argue that Seven supplanted Chakotay as this unobtainable object, but that's another story.
So again, while the obvious elements of their relationship would seem to make this contention seem ludicrous on its face, I think that there are clear signs that Janeway's attitude towards Chakotay is far from unambiguous and could be described as being marked by a substantive measure of passive-aggressive behavior.