John Sheridan and Delenn on B5 was probably the most well-developed and realistic relationship I've seen on TV for awhile. Although it was ultimately cut short, I liked Ivanova's budding relationship with Talia, particularly how it evolved from hatred/contempt in "Midnight on the Firing Line" (S 1.2) to something approaching love by "Divided Loyalties" (S 2.?).
Angel and Buffy's relationship ("BTVS") seemed pretty good and I loved the particularly nasty twist that their relationship took in the middle of S2 to the end of S2 but, as Angel realized by the end of S3, their love would be forever doomed by the reality of his demon/Vampire existence not to mention the unique properties of his Gypsy curse that prevent him from ever experiencing true happiness- with Buffy or anybody else (though it would've been pretty cool to further develop his relationship with that Werewolf in S5).
I'm not sure exactly how it turns out yet but Phoebe's relationship with Cole ("Charmed") seems pretty good although I have a feeling that it will eventually turn out to be equally unworkable due to him, of course, being half-demon (My wife and I are watching S3 on DVD right now)
Sisko's relationship with Cassidy (Yates) seemed well done on DS9, as was Odo and Kira's although theirs ended up not working out in the end. The O'Brien's relationship seemed the most "typical" of the ST relationships. While on the subject of ST relationships, I will NEVER, for the life of me, understand how and why the writers on Voyager greenlighted the idea of Chakotay/Seven. *UGH!!!* I didn't watch the vast majority of Voyager and don't know how it evolved but Paris/Torres seemed pretty decent.
Picard and Crusher on ST:TNG always seemed "right" for each other even though the writers never took it that direction although they gave us some great scenes together in "The Naked Now" and, particularly, "Attached". Riker and Troi definitely belonged together and I'm glad that the writers finally married them by the end of the series (Nemesis).