I use a palm pilot (okay, Centro) with palmwiki for my organization. The wiki is a big help since lets me link documents together for quick reference.
I recommend a couple of levels of notes: Campaign, story, session and person/place/group/item details.
Campaign notes should be like an outline, although I use a timeline mostly. I have the BBEG start a plan and figure out how long each phase takes. Sometimes I apply a deadline (e.g. the stars align one week after midsummer), to motivate the BBEG. I'll note when the major events should take place (Mid May - minions steal Jem of Katmandu, early June acquire Staff of Akbar, late June steal the statue of Akbar, July 10 have statue, gem, and staff at the Lost City of Baquar).
Often I have two or three sets of BBEGs working on plots. Some aren't so much BBEG as they are BEGs or mere EGs so that if they stop Lord Fauntleroy from stealing the orphanage's land for a new cumquat farm then they won't be available to prevent the Gem of Katmandu from being stolen.
Story plans are a more fleshed out view of the antagonists intentions, listing their allies, sometimes which other BBEG they dislike, and their goals.
Session notes are the details you need to run any given game. For me session notes generally consist of a list of the NPCs I expect the PCs to interact with and places I expect them to go with short descriptions, all of them wiki-linked to the pages of the specific NPC or place detail notes.
Detailed person notes are straightforward character sheets with motivation/contact data. I also wikilink it to the places, people, groups, and stories they are associated with. Detailed place notes list the people there (wiki linked to any details) and resources and assets. Groups are like the DMGII organizations but since I've been using this general approach for 10-12 years I never really used their mechanism
The advantage here is that as a GM you can more easily cope with the players going "off script". If they suddenly leave Lord Fauntleroy to go chase the Staff of Akbar, you already have some material ready. Even if you don't have a detailed character sheet for the minions dealing with that part of the story, if you have something as simple as "7th level cleric with doppleganger troops" you can use the stock entries out of the guides.