TiddlyWiki

It's small, it's powerful, it's awesome. TiddlyWiki (TW) is a one-file personal wiki, that can be used as a notebook, a journal, and (quite possibly) everything in between. It does have a few setbacks though. The biggest one, is that some configurations, like the username, and default tiddlers (TW word for post), are stored in the browser as cookies. Which means that if you don't save cookie, or change browser, those settings will be reverted to their default values---not good. The solution is using persistent options. In my case, I store these options:

chkAnimate: true
txtUserName:
chkSaveBackups: false
chkAutoSave: true

One thing that I have *never* been able to do in TW, is installing plugins automatically---it always fails. Which, it turns out, is not big of a deal, because there's a really simple alternative! It doesn't work for some complicated cases, such as SyntaxHighlighter---which, by the way, is a must have plugin if you're a programmer---but for the majority of plugins, it works flawlessly. Another must-have TW plugin, if you write any math at all, is the Mathjax plugin. I installed it via the alternative method I mention above.

It can be customized ad nauseaum. Most of the settings are stored in special tiddlers tagged with systemConfig. This is the case for instance, with CSS (tiddler named StyleSheet, with no tag associated). There are also a bunch of themes, for you to choose from. Have fun!