I like a convoluted campaign. I like having 2-4 subplots running with hints and lures dropped along the way and as the players run through the game, more and more is revealed. Occasionally they complete an arc and have that ‘eureka’ moment when I leave a little clue about something else. It’s great fun and I think they enjoy the non-linear storyline. Giving the group a choice of A or B (and sometimes C) works as they don’t necessarily feel they are forced into plodding along one direction, plus either choice works for me as I’m typically somewhat prepared for each decision (although sometimes I fall short on that).
One tool I’ve picked up for that is Freemind. It is a great freeware program that allows you to construct mind maps. You can save it in a variety of formats, add links and comments, and have a lot of small features to help organize your mind map. Freemind allows you to incorporate all those odd plot lines and keep them organized so your main story can keep on track. More importantly, you can keep all the NPCs aligned to the right arcs.
I use a lot of symbols and color schemes to keep things organized. Bad guys for certain arcs have a matching color to the deeds they are responsible for. I also throw good NPCs into the mix to pair off against villains all tagged with a different color. When I add players into the mix, I also give them small icons that I can tag with particular adventures and NPCs.
The icons allow me to tailor various villains or storylines to a particular player for some more depth in a certain adventure (say an old villain from a character backstory, or a 1 shot solo adventure I ran a player through). Very quickly I can manage a lot of simultaneous arcs, and keep all the story threads neatly arranged. It also is pretty easy to edit, so I can add branches to ideas if new things roll into an arc by the player’s actions.
Give Freemind a whirl. It is a great tool to help congeal those nifty campaign ideas into something organized and readable.