Definitely second Saiunkoku Monogatari. I would agree with recommending the anime over the manga, but I've only read one volume of the manga (since Viz have licensed it I am going to buy it all legally as they release it like a good girl 😀 ) and actually I enjoyed it. I tend to prefer reading manga to watching anime. Still, try both. Only problem is, scanlation status seems dubious and Viz's releases are probably gonna be slow (they seem to be pushing back a few release dates for my favourite series lately, all historical ones like Saiunkoku D:<). Sakujun is awesome though.

I also need to say that I too absolutely LOVED the Blue King in Basara! He was the main reason I was reading it and I got my hopes up about him and Sasara even though I always support the underdog and 99% of the time get disappointed 🙁

Finally I suggest searching the forum for similar threads, I know there have been a lot about enemies falling in love, not quite the same thing but you may well find a few things there.

世界のどこかに必ず
キミの居場所がある筈

Have you tried reading Rave master, Island, Night exile and Crimson cross?

They all make strong implications that the villians fall in love with the protagonist.
Ravemaster for example, has make several implications on villians

Lucia Rareglove or characters that used to be villians ! Let, Jegan, Sighart, Shuda and Reina have feelings or loved one of the main characters in the story
Some of the villians even have their own families and loved ones ! (The King and Hardner)

Island has a main villian that fell in love for the main character that

he almost raped her and sacrificed his life for her. The protagonist is a very intelligent and mature woman, there's no such thing as a 'stupidshoujogirl fall in love with soon to be lover rapist here'.

Night exile and Crimson cross' main characters can be either an anti-villian or an innocent hero.. you'll know the story when you read it.

[img]http://img803.imageshack.us/img803/6167/avvy.png[/img]
Rape is imminent.

Canon, maybe? It's been a while since I read it, so I can't remember if the villain ends up good. But I did really like the main girl.

Azamaru works too, for the first half of the story. Unrequited love for the villain!

*I forgot to mention, Rasetsu no hana by the same author as Canon 🙂 but the scans have halted 🙁

Go to work, send your kids to school;
Follow fashion, act normal;
Walk on the pavement, watch T.V.;
Save for retirement, obey the law.
Repeat after me: I am free.

i second the sundered series

fear death,fear pain,fear suffering what i fear is Nostalgia.

my past memories never ceases to let go.

i second Sali Tayi from Threads of Time. But he is a villain(antagonist) lol, and he stays like that until the end.

But i really loved this manhwa. And i can't bring myself to hate the villain also.

Kakan no Madonna, definitely!

And Jewels, of course. 😃

manga: Inuyasha

Naraku (or Onigumo) loves Kikyou. Unrequited love....sadly 🙁 I love Naraku! He's awesome! Kikyou of course hates his guts...heh....

Bichunmoo is really good... too bad it's not scanlated yet. He's not really evil tho. It's just because of the situation. Think of Masumi. He's the same I think
Also, Four Daughters of Armian many villains fall in love. Really evil woman (but again, it's because of circumstances that she became evil) falls for a man. Then, villain (man) falls for female lead....

Crystal Dragon I think it's quite obvious. He's obsessed with her. They just both didn't know. Here's the evil evil guy, the king of all evil who falls for the female lead, a magician who possessed a strong sense of social justice. While the man is the type of person who slain people without even blink an eye. He just doesn't care about other people. He's creepy
Ruri no Kaze ni Hana wa Nagareru
Hot Blooded Woman creepy guys toying with the female lead the way they like
I think Replay but I maybe wrong since it's been a while
Basilis no Musume I think he's evil enough...
Ten Yori mo Hoshi Yori mo He didn't even realize it
Tenshi no Tattoo kinda

Help! I'm looking for... manga with dangerous guys [url]http://www.mangaupdates.com/showtopic.php?tid=39874&page=1#post594033[/url]

Full Metal Panic! Sigma fits your request only partially but maybe you would like it anyway. I'll explain the differences under the spoiler tag.

Technically, the girl is not the single protagonist, there are two of them, she and the good guy. The girl was in love with the good guy before she met the villain, and even though currently it's unclear whether or not she still is, there is a big chance there won't be any real romance between her and the villain despite the certain tension between them.

Okay, so what fits?

1. The male villain falls in love with the female protagonist. He even admits it out loud.
2. There is a lot of disagreement between them based on personal principles and even the conception of love.
3. She is not spineless at all. She's a strong person though she has her flaws.
4. The villain falls in love first.

The series is a sequel to another series, but only this one contains the plot you asked for, and besides there is nothing that can't be understood without reading the previous one.