I think this fit pretty well what you're describing: S to M no Sekai
(Too bad it seems to be unfinished, even though it's technically "complete.")

Another one:
Jewels
I haven't read that far, but who I think is main dude/villain kills the heroine's parents thinking that they harmed her. This story's almost like Basara, but darker? FYI, the "heroine" can be either a guy or a girl.

Here's some that sorta fit what you want:
Aishite Kudasai, Sensei
Main guy is really obsessed with heroine, probably a little crazy too, though he's not really evil...

Show Princess
It's a love triangle, but I honestly don't know how it will end (haven't read far enough, though I have my suspicions. One of the main dudes is definitely possessive and rather manipulative. (Or maybe both of them are... xD )

Watashi no... Megane-kun
It's a shame this isn't scanlated further. Both characters are crazy. I think the guy more so than the girl. A very unhealthy relationship that I can't stop reading about! The only reason this doesn't quite meet your criteria is that main guy isn't really the villain, there's actually crazier people trying to stop them from being together, besides themselves. If you like this manga, try Yoru Koi by the same author. Obsession galore.

BTW, when I say possessive, I don't just mean "Stay away from my girl" possessive, but "I will do anything to have her, even if she doesn't like it" possessive.

I hope more people post here. I can't get enough of these stories!! xD

Show Princess