At various times there have been mixes and interesting cross-overs between Batman/Bruce Wayne and Catwoman/Selena Kyle.
Bruce likes Selena and they have dated, but Selina finds Bruce a little dull. Bruce likes Selena but wants her to ditch the Catwoman/criminal side. And Catwoman would totally do Batman, sees Catwoman as a crimnal.
Yeah, Batman/Catwoman is one of the best, if not the best example out there. But you seem to be looking for a contained story with an ending and in comics continuity - nothing ever ends - yay! (but really - boo!).
Maybe Rogue and Gambit in the Ultimate X-Men Universe? I know she used to be a baddie (though it was mostly forced up on her) and he is a baddie and she ends up leaving the X-men for him - but I don't remember how it turns out, and again, it's comics, so it never really ends.
Scott Summers (Cyclops) and Emma Frost (The White Queen) but they don't really officially start getting together I don't think until she comes over to the good side (although she's still deliciously bad even when she's good). And again, it's comics, so there's no real ending. The Joss Whedon arc on Astonishing X-Men with them is great though.
Spiderman/Black Cat - though I think Black Cat's now considered a superheroine and their relationship is always on again off again (of course he married Mary Jane, so...)
Though the focus largely became Xena and Gabrielle in Xena Warrior Princess there was also a complicated ongoing relationship with Xena and Ares...and it never seemed to work out, in part because of their different beliefs.
Katara and Zuko from The Last Airbender are a decent example that have a somewhat definitive end, but Zuko comes over to the side of good in the end and thus maybe undoes what you're looking for. There is flirtation and the beginnings of a relationship emerging when he's not yet converted though.
Buffy The Vampire Slayer and Spike are actually a great example. He too comes over to the side of good for her, but he's head over heels in love with her way before he comes over to good - and he actually goes through hell to "become good" so he can be with her. She denies it but is long attracted to and flirting with him even before he "switches teams".
In Willow - Madmartigan and Sorsha (sp?) have a great hero villain flirtation thing going on and it's got a definitive ending, but she converts fairly easily - not much drama to it - it's pretty clear she never wanted to be a bad guy.
In Pitch Black Riddick and Carolyn do a pretty decent hero/villain dance, of course he's really more of a "misunderstood villain type" and she's more of a "not so perfect hero" but they clearly vibe each other. They don't end up together - but only because one of them dies...
I feel like there are a lot of examples of this in film noir - but all fairly stereotypically with the femme fatale character and the detective/hero character - although I think generally the femme fatal is not supposed to fall for the hero and to be really just leading him on. But Vertigo is a decent example of when the femme fatal and hero actually do fall for each other.
The Spirit is rife with Hero/Femme Fatale realtionships, but again, no real endings.
It seems like I'm missing maybe a billion of these - maybe more will come to me. I'll keep thinking.