I've played and run a lot of horror, and it's been hard to dislodge Call of Cthulhu from the top of the list. Here are some other systems I've run horror in:
D&D / 13th Age / Pathfinder: You need to add your own mechanics -- and the nature of high fantasy can make it hard to feel that your characters are really in a state of fear. You can do it, but the system doesn't help.
FATE: This works pretty well, using aspects that express fear, panic, etc. Because Fate defines characters in terms what they are (aspects) rather than what they can do (skills and abilities) it's a naturally good fit for horror, which is all about your state, not your abilities. The reason I still prefer CoC to Fate is that CoC is more simulationist, and I think that helps it feel more real to me.
Monster of the Week: The only PbtA game I've really enjoyed, it's not really horror, but it is fun. PbtA doesn't work for me for horror as you spend too much time out of character trying to come up with three questions to ask about the crime scene and similar. Feels too artificial to capture actual horror. But Monster of the Week is great for a pulp Buffy/Supernatural feel.
Trail of Cthulhu: A good candidate to replace CoC. For me I'm not keen on being able to spend to guarantee success. When I ran a campaign in ToC, it took away a lot from the feeling of despair when players can spend to guarantee they escape, for example. But very close!
Aliens: Great for a one-shot, terrible for a campaign. The panic aspects become bland and predictable after a few sessions ("I rolled 7, hey everyone, add a panic die as I'm screaming at you again") and it doesn't have a lot of non-combat mechanics that are of interest.
Chill: Haven't played enough to comment, but I would happily play again. I suspect I'd like it as much as CoC.
10 Candles: Fantastic. Ton of Fun. Would play anytime. But not suitable for campaign play. I've also played a few other indie one-shot horror games and these have pretty consistently been fun.
Also, an aside:
Thousand Year Old Vampire: This is a solo journaling game that, when I played it, had a strong Anne Rice vampire feel. Generated some actually emotional moments; as an example, I lost both memories and my journal about my first love, and ended up murdering her grandchild on a whim. Writing that scene was quite wrenching.