It seems that this thread is more along the lines of "How does one create a complex plot?" or that is what rycanda is trying to get at.
I think the first aspect is to start from the top and work down. For me, at least, it is easier to start out with whatever over-arching scheme you have. What is the BBEG trying to accomplish? That, right there is the start of it. From there, what allies does he have? What are his centers of power? What does he have each ally trying to accomplish? Do these allies know of each other or do they sometimes work against each others' plans? Create the hierarchy of the bad guys and what they are doing.
After that, you have to create the hierarchy of the good guys. They usually have their own plans that are seperate from the bad guys (trying to recover this artifact or that one) and chances are that the good plans intertwine with the bad ones at some places. For me, these are the places to introduce the PCs to the bad plans and over-arching plot. Of course they don't realize this, but you have to leave them clues and let them go on. Here is where you introduce them to the overall plot.
A technique I use here and one someone else on the boards mentioned once was that I make use of some of my work space. We have some nice big dry erase boards and when I have to get an overall plot down with its main players and motives, I make use of them. Usually I have an idea about the BBEG and work from there. I'll put up the bad guy and his goal (which usually revolves around some item or place) and I'll draw a line. On that line I'll draw the connection which usually amounts to why the bad guy wants it and what he wants to do with it (this is usually left a few words but enough to jog my memory). After that, I put up those allies, power centers, and items that all wrap into the fray.
One of my other points in a complex plot is *not* to railroad. Thats what they did in Final Fantasy VII and a lot of other RPGs and while I still loved them, that isn't what a true RPG campaign is. The PCs have to make their own options and choose which leads they follow. What helps make them complex is that the PCs often explore areas of the campaign you had never considered. They'll go places you hadn't either expected or even planned for, making you add more layers or intrigue.
The other important part of any campaign is not to force anything (often times this applies later in a campaign when characters and plots have been well-laid). If it doesn't fit, then it doesn't fit. Trying to force a particular plot-twist or such is to make it unbelievable. If there isn't a good reason for a good guy to do something evil, then he wouldn't do it. That isn't to say you can't create some dirty secret from his past that might force him to do it, but sometimes something isn't there.
Something else I try to do is leave plot of plot hooks. Sometimes I'll just leave something without any idea of what I want to use it for. I keep a list of these details and items so that I can come back to them later and use them whenever something later comes up. This helps add depth to a game and add that planning aspect of "complexity" that sometimes isn't planned for at all.
This is of course just the beginning. I get the general overall hierarchy, find where the PC's fit into the situation, and then start there with the details. I'll leave the rest for later, only filling in that area and whatever connections filter into that area on my large graph. I have a notebook and one section is just for what I have labelled "Brainfart Ideas", namely ideas I either yoink or come up with that strike me as interesting and for later use. This gives me a list of notions/ideas to pull from. It is one of the most helpful things I have.
Hopefully this might help some. Heck, it might not even be what you want but oh well...I was bored.
