Ooo, this is a fun little topic. Now personally for me, I'm not lumping scare zones in the mix since I feel those are a different beast. As a heads up, I'm basing my decisions on the overall quality of each house, does it offer new things each incarnation or does it rely on the same tricks etc.
1. Scary Tales - Admittedly this hits me on a personal level since twisted Fairy Tales is one of my favorite themes bar none. However even if I disreguard that fact, ST would still be number one since the three houses have been really solid, each one has been distinctively different and they've always brought several new things to it. Even when they repeat one of the tales in a house, they've changed it up in some fashion.
-Tie between Body Collectors and Screamhouse- This one is really hard for me to pick one over the other, so it's a tie. What can I say about BC? They took one of the creepiest characters to hit the airwaves from one of the best Buffy episodes, and made gory, gruesome houses with them. Definitely iconic, though not my personal number one since it does feel like they rely on that spine rip. (That and the past two houses having the same kind of medical theater setting/scares for that scene.) Yes, it's second to Sub Zero's but I feel they can come up with new horrific medical procedures to freak people out. Also, while the first BC was easily HOTY material and Recollections looked damn good, I will say Collections of the Past didn't stand out as much as the other two. While it was the best of the soundstage houses that year, 2008 was the year of Tent City and the Parade building.
Then we got Screamhouse, easily the best Icon house saga. Like with BC, Screamhouse has been wonderfully creepy and gruesome. Admittedly Screamhouse: Revisited was not as strong as it's other two incarnations (After all it was somewhat a rehash of the year before, that and it was pushed aside by houses like PS and Die In.) But the original and definitely Resurrection make this a great house saga.
So that's my top 3, Scary Tales, Body Collectors and Screamhouse. The Honorable mention would be Psychoscareapy, which is a fun saga, but is brought down by having a definitive "dud" of a house. (Echoes of Shadybrook, and I know a good amount who felt Home for the Holidays wasn't up to snuff either.) An' it's had more incarnations then a lot of the other sagas, so for some it's just gotten old.
Though it's still a honorable mention since the original was appropriately infamous, and when it comes to Maximum Madness that is still the best sequel house. That friggin' blackout still remains one of the best effects/show elements in any house.