Based on my own experiences, there are two separate needs writers have for organization.
First is structure. Do you need a pre-existing system to help guild you and flesh out your project? Writing applications, for example, have preset functions and spaces for plots, characters, scenes.
You fill in the blanks, fill out the cards, or connect the dots accordingly. You just start using the software's set workflow and taxonomy, and you stay organized.
Second need is storage and access. Here, you do not want a structure imposed on you. You just want to file your stuff in a way you can reference fast and easy.
My preference, because I am a left-brained geek, is to use a wiki with a structure I create beforehand.
What kills wikis, imho, is lack of curation. You need to tend your wiki like a garden, pulling weeds, moving plants around out of the shade or into it, planting seeds, trimming, watering. Ok, I've killed the metaphor enough.
Point is, you've got to work on your organization system as well as in it, as you go, else you soon suffer information sprawl and chaos.
If this sounds awful to you, then go with the first option and buy something off the shelf that generally takes care of structure for you.
I prefer wikis, and my favourite wiki is PBWorks.com, which at this time is free for non-commercial and personal project use. Thumbs up, as well, on TiddlyWiki and Wikipad, mentioned by others.
Another option is Wordpress. Host your own, or let wordpress.com do it for you for free. Create all the pages you want. Apply categories and tags for easy cross-referencing.
If you prefer a Windows app, then I heartily recommend MyInfo. Version 6 just released, and it offers great features that make it extremely accessible to writers looking to build a base of information for reference.
Another option, if you use MSOffice, is OneNote. It offers more freeform organization on a page than wikis and other software.
Your first consideration is whether you need a pre-existing structure and system, or if you want to create your own. Then go from there.