Koharu no Hibi

Koharu no Hibi is really good manga.

Hiai musou is a new manga out right now and it's also very good so far

Yosuga no Sora and Aoi Sora are both pretty good, if a bit graphic sexually.

Kangerou Meikyuu is another manga but i don't think it's been updated in a while.

Onii-chan Control is alright, and done my one of my favorite manga artists.

There's also Kono kanojo wa fiction desu

Flowers of Evil is one a bit more geared towards females, but good otherwise.

Ana Satsujin is another newer manga.

Choku has a yandere-esque heroine, but i'm going to suggest because it's close enough and amazing.

Abnormal Kei Josei has atleast one yandere heroine. it's not your typical harem manga.

Uwakoi is a really fucked up manga, but not bad.

Finally there's Tokyo akazukin. One of my favorite mangas of all time. It's told from the heroines veiwpoint. Weird manga but damn good.

There's a few others on the list i excluded because the heroines don't have enough plot time or don't follow the yandere mold close enough but if you want to know just say so.