I think the relationship of the O'Briens was the most realistic portrayal. Sure, they had their problems, and it looked like their marriage was headed for a breakup in the middle of DS9, but they stuck with it and worked it out.
I also liked the Kira/Bareil relationship and the Sisko/Yates relationship. Watching both relationships together, we get a good portrayal of how couples can handle interfaith relationships (whether they practice different religions, or the same religion differently). Kira was more orthodox than Bareil, which caused some disagreement early on in their relationship, but they stayed together because they were in love. The Sisko/Yates dynamic was even more interesting because Kassidy didn't seem to have any religious beliefs and showed discomfort at Ben's embrace of his faith. She came around and became supportive, even to the point of at least publicly pretending to practice some of the stuff. (I don't necessarily think a non-believing spouse should feel obligated to act as if s/he believes, but it's a realistic portrayal, since it happens fairly frequently.)
I wasn't into the Kira/Odo relationship at all. I thought it was beautiful when it was Odo's unrequited love for Kira, but I couldn't buy her interest in him. She was uninterested for the whole show, and then suddenly, a hologram convinces her to change her mind. I just didn't find it believable. (Plus, it's really out of character for her to have forgiven him for breaking his promise not to link with the leader of the Founders during the Dominion occupation of DS9.)
I didn't see any chemistry between Riker/Troi, and the less said about Chakotay/Seven, the better.
One pairing that I wish the writers had done more with was Seven and the EMH. They were both at similar levels of emotional development, and they seemed to have a lot in common. They cared for one another, and I think they would have been really good for each other.