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Tomboy is a dead simple note-taking application. It's a lot like sticky notes without all of the clutter and resource-draining. The application lives in your task bar, and you can easily add, link together, and search through notes really easily. The text formatting includes highlighting, spell-check, and bullet point lists; you can even instantly create new notes by clicking on words that LookLikeThis.
For me, though, the best part is all of the plug-ins that are included. Plug-ins exist to show backlinks, to integrate with Bugzilla and Evolution, and to automatically create a 'Note of the Day' to collect your daily thoughts. Best of all, you can use a plug-in to import notes from the Sticky Notes applet.
Tomboy is included with the operating system as a part of GNOME; if you don't have it installed, you can do it in the usual manner. Fire up the terminal and type:
sudo apt-get install tomboy
...and launch Tomboy from the Application --> Accessories menu.