At least in my opinion.
Best FF That Uses Kissing as a Means of Dispute Resolution: Leap, by Kellie Matthews. Due South, Benton Fraser/Ray Kowalski. My high school was full of suburban boys who appeared to have only one means of settling an argument - the traditional method, which inevitably led to mano-a-mano, bloody noses, and, in the fullness of time, the principal's office. If only they'd known that all such arguments could be resolved far more simply and quickly with a kiss. (Although, given my high school, I'm not willing to swear that wouldn't also have ended in the principal's office.) We all would have been spared the lingering ennui of the same old fistfights, and I would, I promise you, have been much more scrupulous about attendance. In this story (yes, I've gotten back to the story), Fraser and Ray argue about risk-taking behavior. And, of course, it leads to kissing. And sex. But kissing first.
Best FF That Uses Kissing to Explain a Confusing Religious Concept Far Better Than Any Theological Texts I've Read: Ineffability, by V, deepsix. Good Omens, Crowley/Aziraphale. This one is short and sweet, and if you don't get ineffability after reading the last line, read it again. Or, I suppose, you could seek out a member of the clergy. But, really, all things considered, I would just go with the re-read. And for those of you feeling squeamish about explicit sex between angels (as opposed to explicit sex involving Angel, which is a whole other fandom), this one does stop at (and start with) just kissing. So if you came here for smut rather than a religious education, you may want to skip this one. (But really, you shouldn't.) Note: this is a time-sensitive link; the host site is closing soon, and we will lose V's site, and Cimorene's site, and a lot of other good stuff. Read it and weep, folks.
Best FF That Uses Kissing as Ominous Foreshadowing: Trust, by the amazing penknife. X-Men movies, Magneto/Xavier. M/X stories just can't end happily. Oh, there have been a few authors who've tried. There're even a few who have succeeded, except that even as you're reveling in the characters' apparent happiness, you can't silence the small voice in your head saying: "If you two knew what's coming..." In this FF, Penknife doesn't try. We see Charles and Erik as they once were, but we also see the future coming in fast, like a fist, and we know how it will end. (For the record, in case you haven't been paying attention: in tears. Well, OK, actually in them developing major ideological differences and spending the rest of their lives on opposite sides battling each other for the title of King of the Mutants, but "in tears" is the short version. To the extent that there can ever be a short version in the Marvel universe.) Lends real poignancy to the kiss, let me tell you.
Best FF That Uses Kissing to Precipitate a Sexual Identity Crisis That Is, Frankly, Long Overdue: The Right to Remain Silent, by Kass and Justine - kassrachel and sanj*. The Sentinel, Blair Sandburg/Jim Ellison. There's a lot of competition in the Significant Kissing category in this fandom, but this one stands out because there's more than one Significant Kiss. Basically, Blair Sandburg goes over his nightly quota of said kisses, and finds himself switching teams before the week is out. Jim Ellison gets bitten and finds himself having sex in a car. All becomes right in the Sentinel universe. Readers everywhere cheer enthusiastically. And I end this set before I develop a tongue fixation.
* Thanks for the link, the_star_fish and kassrachel.