So, DotDG has given us some magnificent examples of cults and groups that the inquisition will be hunting down well into 2009 and beyond, but I must ask- what are your favourite groups? Which do you think are the most characterful and deadly groups and units presented within the book?
Cult of the Year awards 2008
The Vile savants hands down.
Nothing makes player happier then to get stuck in an investigation that ends with Zombie survival.
Adding hazmat decay daemons and father Nurgle into this mix just makes it better 
Personally, I'd have to go with the Temple Tendency, especially as they aren't actually 'evil', or even (necessarily) theologically unacceptable. The forcing the acolytes into political intrigue against the Imperial Cult (whichever way they choose) is simply fun
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If I'm allowed a second nomination, then the Amaranthine Syndicate is really worrying. Seriously gives me chills, and lets me mess around with players 'accidentally' caught up in it. Also, once they know what it is, it is a blatant evil that they don't have to worry about too much after blasting it, although not all members of it are necessarily aware of the true nature of the Principals (so most of the peons, you know, the ones they've actually been killing, will be innocent of everything but ignorance)...
It's realy hard to decide between The vil savants or the Loficians for me., but I think I'll have to go with the Logicians. I just love everything about the Adeptus Mechanicus and tech-heresy, but Zombies are also F'ing cool!
I've had a thing for the Logicians since Edge of Darkness. The Temple Tendancy also stands out, as does Anteanism and Halo Devices, though those last two aren't actually cults.
The Pale Throng. Tranch is where it is at man.
For me, it's the Logicians, because I like the idea to recover a sunken Golden Age of Technology. There are so much possibilities.
On the other hand, the Pale Throng has it's charm, too. You can cause some moral problems in your players, which is only one opportunity ...
tough question.
I like the Logicians a lot, but the night cult has serious potential. And the Menagerie has sufficently lovecraftian overtones to get me thinking about how to use them (shades of the King in yellow!). Anteanism looks like it could also be interesting, if a bit esoteric for my current group.
So I dunno which is my favorite. there's just a lot there to like. but if I had to choose....I'd pick the Night Cult with the logicians an extremely close second.
The Pale Throng are also good, but I figured that I like them simply because of of my players is a Tranch Veteran and I can torment him by having them show up on another world and give him crippling flashbacks.
Logicians all the way! The Brotherhood and the Syndicate are also very much my liking... 
I'm personally a fan of the Serrated Query. I like the idea of a criminal organization that revolves around thinking for yourself. Also, I like that they don't really get down with chaos all that much. It's good to have bad guys who aren't related to the ruinous powers or xenos...they're just nasty, bad people.
I'm surprised at all the love for the logicians. Don't get me wrong, I'm a big fan of the logicians-but why are you?
I also am partial to the Logicians. One of the reasons that I have latched on to them is that they were the first faction that I introduced to my players and I really went to a lot of effort to flesh out the Churgeon from "Edge of Darkness" as a re-occuring adversary. She has hounded them across the the entire sector for their meddling. Needless to say, things are escalating quite nicely. I can relate to the Logicians because I think they are a very "human" faction as well as the Serrated Query. And they are doing the things they are doing, I believe, for the benefit of mankind. As long as they are in control, of course. Tech heresy is just plain old fun and easy to pull off in the Warhammer 40k universe.
Locque said:
I'm surprised at all the love for the logicians. Don't get me wrong, I'm a big fan of the logicians-but why are you?
Edge of Darkness hooked me, firstly. Secondly, well, they're a break from daemon-worshipping cults, murderous aliens and mutant dissidents. I liked the Hereticus Chapter of the book overall because it gave me some wonderful human-based heresies which weren't tied to the dark gods. The ideals their based on look innocuous enough at a glance, if utterly heretical within the setting, which endears you to them slightly. Then they announce their vision of ruling the galaxy with their logical rightness and demonstrate the lengths they will go to to bring about their aspirations, showing you why "logic" and "progress" are such terrible things within the setting. They also remind me of the Illuminati, who I'm sure they derived some inspiration from.
The nemesis from the whole Ravenor series was a Logician, wasn't he?
No, he was merely Cognitae- they were a group of ridiculously smart chaos worshippers
Oops, got the names confused.