Check out Tristania's old releases (Widow's Weed, Beyond The Veil and World of Glass) if you haven't. Also Lacrimosa's entire opus, but I would point out Fassade and Shackal EP (imho Shackal is one of their darkest and most atmsopheric songs). Then also Theatre of Tragedy's earliest - from the eponymous album to Aegis. The Sins Of Thy Beloved's first album, Lake of Sorrow, was also good. Also Trail of Tears - A New Dimenison of Might. Sirenia's first two albums as well.
Also great atmospheric stuff come from Summoning - black metal though, but intensely atmospheric and just brilliant. Try out Stronghold, Oath Bound or their newest Old Mornings Dawn. You should also check Die Verbannten Kinder Evas, a darkwave project by Summoning. And the BM Draugnim and Lustre.
The Gathering' Mandylion is also an album with great atmosphere. In generally The Gathering's music really has it, but after Nighttime Birds they went to experimental rock and weren't metal anymore.
And not metal, but still: Sopor Aeternus's opus, L'ame Immortelle' Gezeiten (EBM band, but with Gezetiten they got a bit more organic and raw), Therion's Vovin (symphonic metal), Paradise Lost's Draconian Times, Anathema's Judgement, the entire opus by Persephone,.... Also bands worth checking: Katatonia, Poisonblack, Fields of Nephilim (Mourning Sun album),.... And oh, definately Dead Can Dance! Really intense and atmospheric music.
Theatres Des Vampires Moonlight Waltz has some good songs too, like Medousa for example, also Nightbreed of Macabria and Pleasure And Pain. The 69 Eyes - Wasting The Dawn also. Some songs from After Forever's Decipher as well (Instrincic, Imperfect Tenses, The Key). Not anywhere near, but Ayreon's song Beneath The Waves is also great, same as Valley of The Queens. But these are just songs, not the whole band's opus or albums are such.
I'm sure you'll find something you like. But I really recomment Tristania, Lacrimosa, Dead Can Dance and Summoning. And as you mentioned Leaves Eyes - I believe their debut, Lovelorn, was their finest work.
Anyone into atmospheric and Gothic doom must listen to Avrigus, they play really atmospheric doom heavily influenced by gothic imagery. If you can find their album "The Secret Kingdom" its a masterpiece.