Hard to say what my favorite horror series is, because I like several different series for different reasons, meaning it would be comparing apples to oranges.
Alone in the Dark, for the original and "The New Nightmare," may be my favorite Western Hemisphere style classic haunted house series.
But Fatal Frame is my favorite Eastern style haunted house series.
Meanwhile Silent Hill is my favorite series for surreal, hellish, psychological horror.
Clock Tower remains my favorite "run and hide" style horror.
And...indeed, Resident Evil, when they actually stick to horror, may remain my favorite "Sci-Fi" horror series.
So...yeah, it's hard to choose any one series. Even with this list, it was hard to do, because every good survival horror game is unique and offers an experience like no other game quite does. Sometimes, that specific game is what I want, and no other game will do. So...in a way, my favorite Survival Horror game of all is "Whatever I most want to play right now."