Might be a bit far fetched and more on the comfy side, but I think both Mushishi and even more so Natsume Yuujinchou fit this category. Some mushi (the main "antagonist" of Mushishi) can be quite creepy. Picture related.
Thematically similar anime include xxxHolic, Ayakashi and Mononoke (not Princess Mononoke), and I think all of those fit too with varying levels of comfy & creepy. I remember their pacing and aesthetic being really comfy, but it has been years since I last saw any of them.
Rozen Maiden is definitely up there as well, for me at least. Some might not agree though. Laplace's Demon is a creepy fella.
Haibane Renmei and even Serial Experiments Lain might do it for some people as well.>>266
Speaking of Gothic, there's always Gosick which literally means Gothic. Too bad I can't really remember anything about it, so I can't say if it was comfy or creepy.