There're a few I'm very fond of atm.
*Owari no Seraph (Seraph of the End) - XU, by SawanoHiroyuki[nZk]:Gemie
*Shiki - Calendula Requiem, by Kanon x Kanon (I haven't seen the series, but like a couple of Kanon Wakeshima's songs, mainly Still Doll and Suna no oshiro from Vampire Knight. Despite its happy, cheerful melody, the lyrics for Calendula Requiem are rather dark.)
*Kuroshitsuji (Black Butler) - Aoki tsuki michite, by Akira
*Kuroshitsuji (Black Butler) - Lacrimosa, by Kalafina
*Madoka - Magia, by Kalafina
*Vampire Knight musical - Kirie toroimen no shirabe, by Akira
*Rose of Versailles - Bara Wa Utsukushiku Chiru, specifically Kamijo's recent cover
*Cardcaptor Sakura - Platinum, by Maaya Sakamoto
*Nightwalker, the Midnight Detective - Gessekai, by Buck-Tick
*Trinity Blood - Dress, by Buck-Tick
I'm sure that there are more, but atm I can't think at the moment.