Just like the title implies, I'm looking for gothic metal bands or songs that have this spooky, scary or unsettling feeling. Something like Mandragora Scream or Virgin Black:
https://www.youtube.com/watch?v=eVUF6f89Aq0
https://www.youtube.com/watch?v=TLYyLYt1BH0

Assuming you're already familiar with Type O Negative, I'll hold off on the obligatory Bloody Kisses rec. There is plenty of good horror/spooky gothic metal out there. Here is a decent handful of albums that I enjoy.

Diabolique - Wedding the Grotesque


Tristania - Beyond the Veil (I find this album pretty similar to that Virgin Black album you listed. There are some lighter and more melodic passages, but a lot of the album has some pretty creepy sounding atmosphere and sporadic bits of some ugly, blackish sounding riffage)


Moonspell - Wolfheart


The Vision Bleak - The Deathship Has a New Captain


Theatres des Vampires - Pleasure and Pain (very similar to Mandragora Scream)


Cultus Sanguine - Shadows' Blood


Monumentum - In Absentia Christi


Sadness - Danteferno


The Nefilim - Zoon

Going to add Light of the Morningstar to this request. If spooky you're after this band delivers. Love it. Both full length albums and the debut EP are excellent gothic metal.

There Are Many Shadows

Lord of All Graves

An Empty Hearse

Cultes des Ghoules - Henbane

Notre Dame?

Those two tracks are quite different so it's hard to know what exactly you're after. One band I'd label as this kind of spooky gothic is Darkwell, who put out one fantastic album in the early 00s:

https://www.youtube.com/watch?v=CEq4ZKHu3g0
https://www.youtube.com/watch?v=Go61w3WLvgs
https://www.youtube.com/watch?v=SnmDepRXtS8