First of all: For any setting, five distinct groups is the best starting place. This does not mean the setting should only ever have five unique subgroups, it means that there should appear to be five distinct factions that the characters will have heard rumours of by the end of the first story. Subgroups, controlling interests, all of that comes later.
A suggestion that Ken borrowed from George Orwell is to have three groups, each being beaten on by the other two. We can expand this easily enough to five groups. A fully connected network of the groups:
Assume that the exterior links are overt hostilities between the two groups. There is a bidirectional hostility between them. Each group is also attacking one enemy without retaliation and being attacked without realising, as represented by the unidirectional internal links.
% - Groups know of each other and are engaged in hostilities.
# - The row group knows of the column group and is attacking them without the column group necessarily knowing.
$ - The column group knows of the row group and is attacking them without the row group necessarily knowing.
That's all well and good in theory, but does it work? Does it translate?
Let's pick some roughly Deus Ex-ish groups. This is likely now how things will play out, but we shall see.
A - United Nations military forces, UNSCIT and UNATCO
B - NSF
C - The Thule Society
D - The Vatican
E - US Government agencies
From the point of view of the UN, it's in open cold-war level hostilities with the US government and it's agencies and the NSF, a worldwide network of anarchists that are concentrated in Hong Kong. It knows of the Thule Society (the network connecting and organising a large number of neo-Nazi terrorists around the world) but is targeting supply lines and leaving sleeper agents rather than tipping their hand. It doesn't believe that the Vatican is a major player, but the Holy Church's watchers are keeping a close eye on the UN forces and are feeding them enough misinformation to keep them away from their own activities.
Expand that to cover all the groups, and you have the basis for a conspiracy-laden world for your characters to be thrust into. Of course, you should detail the group the characters belong to, detailing a minimum of three sub-groups and working out who is pulling the strings behind the scenes. Once you've worked out the agenda of all the subgroups there, move on to whoever the PCs will be facing. Detail is the key, and if you throw out a random name be sure to note it down. If the players investigate, great. If not, it will come back for them.
In general, a story should only work with a couple of these threads at a time. See what you can drop as clues, and see which your players pick up on. From there, you know the parts that you need to work on detailing, and the parts that you can leave for a rainy day.