I've been searching for some manner to organize all my mountains of notes, timelines, character summaries...etc etc for quite a while now, and (thanks to Lugh) I think I've finally found something worthwhile called Liquid Story Binder. It's open-ended enough that it satisfies most of the niggling annoyances that have made me toss aside other similar programs.
Of course, Lugh just HAD to point it out right in the middle of my Nano writing when I had already thoroughly submerged myself under piles of long-hand notes and printouts. But well...better late than never. It only uses up about 15 megs of memory to run, which is way less than freaking firefox. So, no technical problems even with 342545642 windows inside story binder open. Anyhow, I took a quick run through the help and got started inputting all my notes; six hours later I can happily browse through all my characters and masses of notes on the fly. The search feature is also quite adequate for my needs and you can search through specific areas quite easily.
Only two drawbacks that I'm going to note: drawback #1 is of course that LSB XE is shareware, which means you have thirty days of trial(non-consecutive), then you have to buy it to keep using it. It's a measly 45 bucks though for as many personal copies as you want (for those of us with desktops and laptops who interchange frequently) and you get updates for free for life as far as I can tell. Drawback #2 is that the word processor inside LSB, while functional, holds not a candle to Microsoft word as far as paragraph formatting, and spell/grammar checking go. And when you have hundreds of pages you're trying to format at the same time, that becomes somewhat important. I should mention that it does allow exporting in .rtf, but I have had no trouble simply using storyboard for everything but the actual chapter writing, which for the foreseeable future, will remain in word.
All in all, once you've figured out how malleable everything in the program is, it becomes rather enjoyable to use and much more convenient than lugging around binders to a coffee shop when you want a change of scenery for writing. You can also install LSB on a usb drive and use it on any computer...which is also kinda neat...not that I use that feature...
Here's a link: Liquid Story Binder