Cults are a nice source of bad guys in most game settings. You can toss them into just about anything with a little work and thus create a small network of like minded individuals that the characters have to deal with. However I do see one thing that a lot of folks do that just doesn't make much sense to me. When they go and name this group they call it the 'Cult of whatever' or some such. Even the NPCs call it by that name. Personally I don't see a lot of groups coming out and saying “Hey look at us! We are a cult!”.
Cults have a negative connotation attached to them. Just hearing the word 'cult' and people start to think of bad things done in secret places for even worse reasons. Now why that may actually be what your fictional cult does, they wouldn't want everybody knowing about it. Give them a name that seems a bit more innocent but still adds that bit of mystery. An especially useful thing to do is chose something that ties into an already existing established religion. Then they may simply be thought of as being a different demoniacal of that. Mostly just like all the rest with a few small differences.
A few good words to use would be: Order, Sect, Following of, Chapter, Body or Clan. All of these tone down that immediate thoughts of bad reputation a few notches. They also won't make the characters as nervous about them right off the bat.
Now again they probably don't go around advertising themselves either. So this isn't a name they are going to be hanging on a shingle out in front of their homes. After all if they really weren't a cult of baddies then they wouldn't actually be that useful would they? Therefore keeping their group hidden even among the locals would be of importance also. Only when they feel they are talking to a likely recruit or potential ally would they reveal who they are. Even then they would probably sugar coat their activities and beliefs. Then urging the person they intrusted with the information to keep it secret as well.