I definitely agree with Picard/Crusher and Janeway/Chakotay. There was definitely chemistry there that could have been further explored. Hell, the TNG episode "Attached" should have sealed the deal with P/C and yet it never happened. At least the novels finally had the nerve to tackle the P/C relationship. J/C fans would feel bittersweet about the exploration of a romance between Janeway and Chakotay in the VOY novel Full Circle
As much as I prefer Picard with Crusher, I will say that his relationship with Neela Darren in "Lessons" was interesting and well-executed. She seemed to be a good match for Picard, and it's a shame that she only lasted for one episode.
I loved the flirtation between Jadzia and Bashir, but I honestly never expected them to get together. I kinda liked the way they played Bashir as a lovestruck puppy following her around. I think she enjoyed the attention but would have never considered him as a potential suitor.
I have to say that I was a big fan of the Doctor/Kes relationship. I think that could have blossomed into something sweet. Those two also had great chemistry. I didn't particularly like how the Doctor became so attached to Seven of Nine in the later years; I much preferred him with Kes and it's a shame that their relationship didn't have an opportunity to develop further.