Definitely Niles Crane and Daphne Moon.
Man, I miss
Frasier.
Agreed, although I think the show did jump the shark once they got together. My favorite episodes of that show are often the ones where the smoldering sexual chemistry is just beneath the surface and they pull the rug out from under us at the last minute, like "Moon Dance."
2 other will-they/won't-they couples that I invested years into rooting for are
Odo & Kira Nerys on
Star Trek: DS9 and
Wesley Wyndham-Price & Winifred Burkle on
Angel.
I have nothing but the best hopes & wishes for
Rodney McKay & Jennifer Keller on
Stargate Atlantis.
I was a huge fan of
Dave Nelson & Lisa Miller on
NewsRadio. (Season 5, despite being Phil Hartman-less, might have been tolerable had they had Dave & Lisa get back together rather than marrying her off to that obnoxious Johnny Johnson.)
For a couple that nearly killed each other as often as they loved each other,
Dick Solomon & Mary Albright on
3rd Rock from the Sun. That was some great insanity right there.
Oh, and an honorable mention for
Cordelia Chase & Alan Francis Doyle on
Angel. I'm sure they would have made beautiful music together had he not died a few minutes after she agreed to go out with him. ("I guess now we'll never know if this is a face you could learn to love."

)