Any manga/manhwa/WN/LN where the villain tries to or becomes romantically involved with the hero. Preferably seinen or josei level of maturity but shounen and shoujo are fine if that's all you know. No yaoi/yuri.

Things I've already read:
Superior
Superior †
Basara
Jewels

These don't really count because the "enemy" was not a person that has done evil acts, but was related to those that did the evil but were not villainous themselves:
Maoyuu Maou Yuusha
Reimei no Arcana
Zettai Heiwa Daisakusen

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Otoyomegatari
Dungeon Meshi

Jewels - Pretty cruel guy. Interesting story but rushed near the end.

Thanks SilverStorm it was a good read even though the ending was rushed as you said.

Also bumping after 7 days of nothing.

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Otoyomegatari
Dungeon Meshi

Well if you are willing to be a bit patient you could try Project Arms. About a third of the way through the manga the villains kidnap one of the female leads as bait for the heroes to walk into a trap. It takes them a really long time to get to her and in the mean time the villain assigned to watch her falls for her.

Tough one, there's The Tarot Cafe and if you don't mind webcomics there's also Next Town Over.

Must Read Webcomic:
Unsounded

Lists:
Reading
Complete
Western Webcomics

Kyuuketsu Yuugi
The Legend of Maian
The Legend of the Sun Knight has it as well but I don`t think that the manhwa has gotten so fat so only the novel version.
Spirit Circle plays it to some extend
Maou no Hajimekata mindless borderline hentai manga but technically it has bad guy and hero type character intimate relationship
Gu Fang Bu Zi Shang
Dai Zhan Tian Shi

Masca -I dont really remember well but i think it was something like that..
seimaden- kind of
jiraishin some chapters had that plot.... i am not really shure if Ida can be considered as a stereotipical "good"

Vampire Game

Hobbies include impersonating fictional characters and sucking on ketchup packets.

Bump to see if there's anything new or anyone else has something to add.

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Otoyomegatari
Dungeon Meshi

Watashi no Ookami-san and its sequel Dear, though both are shounens and read like shoujo.

There's a side-pairing in Hekikai no AiON like this, but it's unrequited. And, again, the manga is shounen.