I am now evaluating TiddlyWiki as my reference system, as a replacement of my text-files stack.
For those not familiar with TiddlyWiki, it is a bizarre but mighty single HTML file which can work just like a Wiki. You can store this little HTML in a USB stick or your iPod and you got a Wiki-to-go. You may download yourself a copy of this HTML and try yourself. It is free.
The Pros and Cons of this TiddlyWiki are

pros:
1. Portability, you can edit TiddlyWiki with any POPULAR browser on Windows, Mac and Linux. It is just a HTML file.
2. Wiki-based organization system.

cons:
1. You can easily get lost this system. Partially because the UI and presentation is too messy. Not as classy as Media-wiki based system.
2. It supports POPULAR browsers for editing. Notable omissions included Safari, Opera and Shiira (My favorite browser right now). I have to use Camino in Mac OS X to edit it. (Firefox for Mac OS X is still a bloatware. I don't like it.)

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